Updated January 2024.
CONGRATULATIONS ON BOOKING A TRIP TO TOKYO! I'm absolutely thrilled for you and wish I could personally show you around, but since I can't be there in person, I wanted to share some of our favorite spots from our recent visits. Tokyo is a special place, and it's a city that never fails to amaze us. There’s a feeling we get when we return to Tokyo that’s hard to put into words (I’m tempted to make up a word to describe it), but it’s a high that keeps drawing us back. As much as the city evolves, there are so many places on this list that bring us joy to revisit. If you have any questions or need advice as you plan your trip, please don't hesitate to reach out. Japan is my passion!!
General Travel Tips
Pocket WiFi: Consider renting a WiFi hotspot before your trip. I’ve tried both Pupuru and Tep Wireless. Pupuru (more fun to say) is perfect for Japan-only travel and can be delivered to your hotel in Japan, complete with a pre-stamped envelope for easy return (must be returned in Japan). Tep Wireless provides coverage across various Asian countries, and you can receive/return in the US. Tokyo generally has reliable LTE/5G coverage, but relying on apps like Google Maps and Google Translate 24/7 can sometimes be tricky without a consistent WiFi connection.
Navigating Tokyo: Tokyo is basically a city of cities. It’s sprawling. Make sure you download a Pasmo or Suica card (they function the same, so you pick!) to your phone before you touch down in Japan. These cards are not only your ticket to Tokyo’s world-class subway but also a digital pay card that is accepted at various places like convenience stores, restaurants, vending machines, taxis, etc. Just look for the little Pasmo or Suica logo. You can find step-by-step instructions on how to download and install a Pasmo here and here. You will need to have ApplePay set up.
Once you’re in Tokyo, you’ll find the subway incredibly easy to navigate and English translations on every sign. It puts all other mass transit to shame! Stations are organized by color (i.e., Ginza is the orange line), and all of the stations are numbered. So it’s helpful to know the color of the line and whether the number of the station you’re heading is going up or down. Google Maps also gives extremely detailed instructions, down to which car you should ride for a faster exit or transfer. So if you get lost or confused, maybe it’s you!
Subway stations are like underground cities, so be on the lookout for delicious restaurants, bakeries, and other shops. Some of the best food and snacks are down there! When waiting for the train, do as the locals do. Line up single file and allow people to exit before boarding. It’s crazy how easy it is to be courteous! During weekdays, some train cars are designated as women-only, so gentlemen, please take note. Additionally, keep an eye out for train cars with milder temperature settings if you prefer low air con.
While taxis are convenient, they can be expensive. You can easily have your hotel hail one for you or flag down one of the iconic doily-laced Toyota Crown taxis on the street. If you’re looking for a taxi on demand, Go Taxi is the Japanese equivalent of Uber. Uber does exist, but Go Taxi has a larger and more reliable network.
Politeness & Language: Japanese culture is known for its graciousness, politeness, and deep respect for others. While the language barrier may be a concern, I’ve noticed that it becomes less of an issue with each visit. You’ll find that most Japanese people genuinely want to help you, and they’ll try their best, even if they don’t speak a word of English. Google Translate is your friend, but it’s also not a bad idea to learn a few basic words/phrases in Japanese. Additionally, I suggest carrying your hotel’s business card with the address written in Japanese so you can always communicate where you are staying.
When you’re on the ground, BE ON TIME. It is offensive to be late to any appointments or reservations, and they may choose not to serve you. Don’t risk it! If you’re eating omakase, remember not to wear perfume. Eating uses all five senses, and the Chef may kick you out for interfering with that. Be prepared to experience some of the most delightful and hospitable experiences ever! It’s common to be escorted out of stores and restaurants with a respectful bow(s) as you leave <3
Restaurant Reservations: It is crucial to plan ahead in Tokyo. Many of the acclaimed restaurants require reservations (some are referral only) and often open their books 3-6 months in advance, so manage your expectations to how much time you have for planning. An increasing number of restaurants take online bookings through platforms like TableCheck, Tableall, Omakase, and Pocket Concierge. I still think having a hotel concierge or a Japanese-speaking contact to assist is your best bet. Locals rely on Tablelog for restaurant ratings, not Google, Yelp, TripAdvisor, etc., so cross-check any restaurant reviews there. There are certain restaurants that are popular with the Americans (i.e., Wagyu Mafia, Shima Steak, Sushi Saito); don’t be bummed or think you’ll have a compromised experience if you can’t get in at those places. The food scene in Tokyo and Japan is E-L-I-T-E, like truly. There are over 200 Michelin-starred restaurants in Tokyo and AMAZING food in every nook and cranny. Do not hesitate to try restaurants in the subway or train stations, basements of office buildings, department stores, etc.
If you visit during the Christmas-New Year break, be aware that many restaurants are closed the first week of January. Hotel restaurants (which are still some of the best in the world!) or outposts of Western restaurants may be your only choice.
Restrooms: This section is for us ladies!! Rejoice!! There is very little to worry about when it comes to having to use public restrooms in Tokyo. Most public restrooms, including subway stations (yes, seriously), department stores, and public parks (yes, seriously), are meticulously maintained and regularly cleaned. To add to our comfort, many of them are equipped with the legendary Toto Washlet, aka Team No Cold Seats. To give you an idea of how seriously they take public restrooms, Tokyo has a city-wide project called “Tokyo Toilet,” where renowned Japanese architects have designed unique public restrooms.
While I’ve seen these less and less, there might be a few places with squat toilets (I had no idea what to do!). So, I suggest bookmarking this Wikihow guide just in case!
Shinkansen Train: If you’re planning a longer trip, traveling on the high-speed Shinkansen bullet train is a must. Kyoto and Osaka are the easiest trips from Tokyo. I recommend purchasing tickets in advance and opting for reserved seats. I used Rail Ninja to book online, but a hotel concierge can also do this for you too. Buying tickets at the station the day of is possible, but if you are visiting during a holiday period, you absolutely want to buy tickets ahead of time. Trains will sell out. When leaving Tokyo, sit on the right side of the car to get the Mt. Fuji view and the left side when you return! We’ve booked both first-class and standard cars, and honestly, both are great. Standard seating on these trains is better than anything you would experience in the US. There are baggage weight limitations, and you will need to reserve space for larger bags. If you are traveling with a lot of luggage that exceeds the restrictions, consider using one of Japan’s reliable luggage forwarding services.
Hotels
Hotels in Tokyo are exceptional! They’ve totally ruined me and set the bar so high. Splurging on a luxury hotel is well worth it, and having access to an excellent concierge team can greatly enhance your trip.
Four Seasons Otemachi: We love this hotel! It’s brand new and located near the Imperial Garden. The hotel lobby is on the 39th floor of an office building (the hotel rooms are up from there), so the views are amazing. There isn’t much to explore in the immediate neighborhood, but it is extremely convenient for getting to other parts of the city by subway or foot. The only thing the hotel is missing is a dry sauna and a cold plunge (there is a steam and a warm pool). The only thing! The gym and spa areas are excellent, but just wish they offered those two things.
Prince Gallery Hotel: I’ve stayed here twice and had great experiences. It’s also brand new, very high-tech, with gorgeous views and an impressive gym and spa (they have a full range of pools and saunas!). The hotel is associated with Marriott, so there could be additional benefits or upgrades if you have status. The hotel sits at the nexus of three major subway lines that you will frequently use. The concierge team was able to get us some tough reservations.
The Palace Hotel: My husband stayed here on a business trip and was raving about it. I would definitely book here!!
Park Hyatt Hotel: Iconique! It's a fantastic choice for a short stay or a relaxing night before departing Tokyo. However, it is a bit out of the way and not close to a subway line, which can be annoying to deal with if you’re staying for more than a few days. If you don’t stay here, you must at least go to the bar or restaurant, more on that later!
Mandarin Oriental: This hotel is always recommended by friends and travel publications, so I feel the need to acknowledge it, but my personal experience here wasn’t exceptional.
The Tokyo EDITION Toronoman: This hotel has a very cool scene and the best-dressed guests I’ve seen in Tokyo. If you’re a fan of the EDITION brand, you’ll likely enjoy your stay here. However, if you’re in pursuit of a more authentic Japanese experience, consider the options above. I also must warn you that the closet in our room was extremely small. If you’re like me and unpack like you’ve signed a three-year lease on your hotel room (regardless of how many nights), you’ll find it difficult to get organized and settled. You also have to pay to use the sauna, a crime!
Other hotels that have been recommended or are on my radar are Aman Tokyo (divine!), Andaz Toranomon Hills, The Tokyo EDITION Ginza (designed by Kengo Kuma, but not sure what the closet situation is there), TRUNK(HOTEL) in Yoyogi Park (look amazing!) and the sister brand of Aman, Janu Hotel, located in the new Azabudai Hills opens March 2024.
Activities
When I travel, I try to hit the essential tourist spots but also prioritize places unique to Japan with a strong emphasis on design, furniture, fashion, vintage clothing, and sky-high views. We also walk a ton in Tokyo. I’m talking 10-13 miles every day. Some of the activities or neighborhoods listed below are things we’ve stumbled upon during a long walk. This is not meant to be the end-all-be-all of what to see, and trust that you will find the major tourist attractions and new places on your own!
Mori Art Museum and Observatory (Roppongi Hills): The rooftop observatory alone is worth admission. Go around sunset on a clear day and enjoy those selfies with Fujisan!
21_21 Design Sight (Roppongi)
Takeshita Street (Harajuku): Worth a stroll, even though it’s very touristy. You will see many crazy outfits, vendors, and cat/owl/animal cafes. The cafes are unique to Japan, so you decide if you want to stop in one. I thought they were kind of sad and a little awkward.
Meiji Shrine/Yoyogi Park (Harajuku): One of my favorite places in Tokyo.
Togo Shrine (Harajuku): Serene neighborhood shrine. If the two places mentioned above are too busy.
Shibuya Crossing (Shibuya): You absolutely have to do this. It’s wild how many pedestrians and cars do this crossing every time the light turns without a single honk or raised voice! Fellow dog lovers, plan to pay your respects to Hachiko at his statue in front of Shibuya station. For the story, click here.
Electric Town (Akihabara): The epicenter of video game culture. Go in and play at one of the many video game “casinos.”
Imperial Palace & Gardens - So beautiful to walk and run through. There is a 5KM loop that goes along the perimeter that I run every visit! Most hotels will have a running map, but this website has a map and some etiquette to follow while running/walking the loop.
Tokyo Skytree: Only go on a clear day. Otherwise, it is okay to skip!
Senso Ji (Asakusa): A very popular and colorful Buddhist temple. I like this one the best. Just note that it gets very busy around the New Year and other holidays.
Nezu Museum Gardens (Minato): A fine arts museum with pre-modern Japanese and East Asian art that is worth checking out, but the gardens are definitely the best part! Make sure to go on a day when you can enjoy exploring the grounds.
Gotokuji Temple (Setagaya): The famous good luck cat shrine. It’s a bit of a trek, so saving this for your second or third visit to Tokyo is okay.
Team Lab: I know these experiences are viral, but I found it to be a tourist trap. Most of the sought-after rooms have been spoiled by Instagram, and there are so many people standing and jocking for “the shot.” Art is not my forte, but I can say with certainty that there are better art experiences in Tokyo. However, they have a new exhibit opening in Azabudai Hills.
Azabudai Hills: Speaking of Azabudai, it’s a brand new neighborhood in Toronoman, designed by Heatherwick Studios. It is some of the most inspiring architecture and urban design. You’ll be jealous we don’t have this in New York!
Atago Jinja (Toronoman): A Shinto shrine in the Toronoman neighborhood. Access it through the famous Stairway of Success. As the name would suggest climbing up and down the stairway is meant to bring you career success!
Rabbicour (Ginza): The tap water and my hair are the only things that disagree when I’m in Toyko. I found this fabulous Alice in Wonderland-themed Japanese Head Spa in Ginza. The staff is kind and in costume. Be prepared to use Google Translate to communicate.
WA SPA (Ginza): Combat sushi face with a facelift massage at Wa Spa or try a facial with Glow by Tomoko, one of the best facials I’ve ever had.
Shopping
Luxury/designer shopping in Tokyo is my favorite thing to do! There is often a significant discount shopping in Japan vs. the US (you gotta spend money to save money!). If you are eyeing something designer, wait and buy it in Japan! There are multiple flagship-sized designer stores, and they often carry inventory that isn’t available in the US. Start with the locations in Ginza first and then visit others as necessary. Remember to bring your passport and ask to buy duty-free. Most price tags display a duty-free price, which is what you’ll be charged, eliminating the need to go to a counter for cash back or services like Global Blue. I’m not entirely certain about the protocol for declaring items when you leave Japan, but at Haneda Airport, the customs desk is just past security, and I just tapped my passport on their scanner (did I *need* to do that? IDK!). For a deeper understanding of Japanese style and fashion brands, I highly recommend reading Ametora.
Department Stores (in order of preference and location):
Matsuya (Ginza)
Iseten (Shinjuku)
Dover Street Market (Ginza)
Takashymia (Nohombashi)
Takashymia (Shinjuku): This is the big one!
Misukoshi (Ginza)
Ginza Six (Ginza) - This building is incredible!!
Kitte (Maranouchi)
Barney’s New York: Not kidding! Barneys is alive and well in Japan. If you’re feeling nostalgic, visit one of the many locations in Tokyo!
Omotesando & Aoyama: Besides Ginza, this area is my favorite to shop. You can spend several afternoons wandering the streets between these two neighborhoods. The area is also known for its amazing architecture. For a list of the amazing buildings to experience, click here. I also check Dezeen before any trip to see if there is anything new and exciting to check out.
Cibone: Japanese homeware store in the GYRE Building. Just opened in Brooklyn!
CFCL: Also in the GYRE Building. Brand by the designer Yusuke Takahashi, the former head of ISSEY MIYAKE Mens.
Omotesando Hills (a mall)
Panasonic Beauty - For next-level beauty and hair tools
This second-floor Blue Bottle Coffee has the most serene deck. Perfect for a coffee and a rest.
Cat Street & this section of Harajuku Street: No real destinations to call out, but I have always loved walking on both streets and popping into the various shops. The link will take you to the APC store, which is a good place to start. The streets in the surrounding area are all very cool.
Daikanyama/Nakameguro: These are really awesome neighborhoods that are very residential and quiet. I actually think they call it “Little Brooklyn.” I love the Arts & Sciences store, T-Site, SML for Japanese pottery, and Post O’Alls (men’s). I haven’t been but want to go to J’Antiques.
Vintage: I love vintage shopping in Tokyo. Vintage is a serious specialty, and I am always so impressed with the carefully curated selection and the quality of vintage pieces. Tokyo offers a fantastic range of unique American and designer vintage, often at a very reasonable price. This article is an excellent guide to some great vintage shops in Tokyo. In addition to the stores mentioned in that piece, I would suggest RagTag (similar to The RealReal) in Harajuku, which is great for more contemporary fashion pieces.
Shimokitazama, aka “Shimokita:” I would live in the neighborhood if I lived in Tokyo! It’s known for being one of Tokyo's more “boho” areas, with many cool vintage and antique stores. Slowly walk the streets of the vintage district and hit Reload, an indoor-outdoor shopping mall with some great stores and cafes. I suggest APFR for delicious fragrances and this home goods store.
Japanese brands with multiple locations: Beams, Kapital, Tomorrowland, L’Appartment, NANGA (great down jackets), Nanamica (another great outerwear store).
Food
While in Japan, I typically stick with the five main food groups, tuna, tempura, tonkatsu, noodles, and Kobe beef. However, during my recent visits, I’ve ventured into other cuisines. In Tokyo, you will find some of the best French, Italian, Chinese, pizza, etc. in the world. It might be worth considering booking a non-Japanese meal for one or two nights during your stay.
Breakfast:
Tsukiji Fish Market: You can do the early morning tour or just wake up and have tuna for breakfast! I love Sushi Zanmai (Hoten location), which is “one block up” if you enter from the Harumi Dori/Shin Ohashi Dori corner. I recommend ordering the tuna chirashi bowl and a few pieces of tuna sushi/sashimi to accompany it. Sushi Dai is also really popular but regularly has a 3+ hour wait. I have heard great things but have not been up for waiting. Sushi Zanmai doesn’t take reservations, but it is much bigger, and the line is efficient.
Bills (Multiple Locations): My favorite locations are the restaurants in Ginza and Omotesando. The hotcakes (pancakes) are a must. Oh, and the circular banana slice-looking things on top are butter, so don’t eat the whole thing. You must make a reservation!
Brunch Buffet at NY Bar and Grill Park Hyatt Hotel (Shinjuku): There have been many times in Tokyo when the food almost reduced us to tears. The brunch at the Park Hyatt was one of them. It’s pricey, but once you see the spread, you understand that it’s worth every penny. Go on your last morning in Tokyo, and you’ll have to be physically removed.
Dim Sum Brunch at Sense at the Mandarin Oriental (Nihonbashi): If you’re looking for something more upscale and dim sum-y, we recommend the brunch at Sense. The food is delicious, and the view from the restaurant is awesome.
Cafe de l’Ambre (Ginza): This is a must every time we visit, and the same people are working there every time. It’s a cash-only old-school kissaten (coffeehouse) perfect for a mid-afternoon caffeine hit. Most coffees are served as espresso or as hand-poured or shaken drinks. I highly recommend ordering the Blanc et Noir.
Lunch: *Note most restaurants end their lunch service by 2-2:30pm*
Ramen:
Tokyo Ramen Street in Tokyo Station: I thought this was tricky to find, but once you find it, pick any shop. Don’t get intimidated by lines. Things move quickly.
Afuri Ramen (multiple locations): These are all over now, but it’s still great. We like the location in Harajuku the best.
Ramen Nagi (Golden Gai): Unique fishy broth that is delicious. It only has a few seats and a very steep set of stairs to get in.
Kikanbo (Kanda): It can be spicy but so flavorful
Ippudo (multiple locations): This is now in the US, but I still suggest visiting!
Soba/Udon:
Abura Soba (Akasaka): Known for their oil noodles, not noodles with broth.
Kanda Yabu Soba (Kanda): Elastic waistband preferred! There is a chance you will have to sit at a tatami-style table.
Godaime Hanayama Udon (Ginza): Known for their delicious flat wide noodles
Tonkatsu:
Maisen (multiple locations): A “chain” tonkatsu restaurant you must try! Easy to find! There is a location in basically every area of Tokyo.
Tonkatsu Wako: Located in the Iseten in Shinjuku. Excellent!
Other spots that have been recommended but haven’t been tried were Tonki and Butagumi.
Curry:
Rojiura Curry Samurai (Multiple Locations): I went to the one in Shimokita and loved it. Suggest ordering a mango lassi to accompany your meal.
Oyakodon (Chicken and Egg Rice Bowls):
焼鳥 ここりこ庵 六本木ヒルズ店 - This place!! We randomly found it when we were absolutely desperate for food, wandering around Roppongi. So delicious and cheap. It jolted us back to life.
Pizza:
Savoy (Multiple Locations): Exceptional Neopolitan pizza! We accidentally ate 4 pies for lunch. You can skip the Marinara pizza, but I’m telling you now: you want the cheese on the Margherita. The menu only says that they have two pizzas, but there is always a special and some off-menu pies that some people seem to know from the original location — a Bianca pizza and a tuna pizza that comes with a large serving of tuna in the center and a side of wasabi. It was insane. There are a few SAVOY locations. We went to the one in Azabujuban (linked above), and there was no line and a decent amount of seating.
Pizza Bar on 38th at the Mandarin Oriental: I haven’t been, but it was recommended by a few people on the ground.
Snacks
Depachika, aka Department Store Food Halls: I can’t describe how amazing these are. Every department store has one, usually on the basement level, with many options. My favorite is the one in Matsuya Ginza, but I also suggest the Mitsukoshi, Isetan, and Takashimaya food halls. All of the locations have them.
Rose Bakery at Dover Street Market
Omoide Yokochō aka Memory Lane (Shinjuku): Sit in any stall with an open seat and enjoy the variety of yakitori. I found this guide to be helpful. Bring cash.
Convenience Stores: The egg salad sandwiches and any flavored potato chips from Lawsons and/or 711. We learned about the sandwiches through Anthony Bourdain and David Chang, but they live up to the hype. I always grab a few for the plane back.
Dinner (The Main Event)
Steak
Ushigoro S. Ginza (Ginza): I booked this on the recommendation of the Four Seasons concierge, and they did not lead us astray! I opted for the K menu (short for King), which was 14 courses (some were small bites). I thought it offered an excellent selection of cuts and preparation styles, as well as a dessert. All reservations are for a private room; there is no main dining area, and the waiter will cook everything to your liking right at your well-ventilated table. The pièce de ré·sis·tance was the Chateaubriand cutlet sandwich. So much better than Shima Steak! Just know that there are a few restaurants by this same group with similar names. This one is in the Ginza 777 building.
Innocent Carvery (Akasaka): The name is silly, but the yakiniku Wagyu tasting is not. It was a great experience, and the steak was phenomenal. Many places like this exist, so feel free to explore other options. You can book a reservation online.
Peter Luger’s Tokyo (Ebisu): Yes, it’s the same steak they serve in the US. No Japanese Waygu is served here. I’ve never been to the Brooklyn location, so I can’t really compare, but it’s apparently a copy-and-paste version in Tokyo. The decor will transport you back to the US, as will the portion sizes.
Shima Steak (Nihonbashi): We’ve done it and DAMN, it was so good. Don’t go home without one of their steak sandwiches to eat the next day, but only if you can refrigerate it!!
Sushi
Sukiyabashi Jiro Roppongi Hills (Roppongi): If you haven’t watched Jiro Dreams of Sushi, you must before arriving in Tokyo. It will make you that much more excited for an authentic Omakase experience. This is Jiro’s son’s location. We were lucky enough to get a reservation through our hotel’s concierge, and it was an A+++ experience. Chef speaks English well and is very personable and funny. Since it is only counter seating, be prepared to chat with him throughout the whole meal.
Sushi Kuriyagawa (Ebisu): This has become our go-to omakase spot in Tokyo. You may have trouble finding it when you arrive, but just know it’s on the basement level, and you’ll see the sign at the top of the stairs.
Ichiyanagi (Ginza): This was our first omakase experience in Japan. I think the dinner was wonderful?? There was an earthquake while we were eating, and that’s all I can remember.
Tempura:
Tempura Miyashiro (Naka-Meguro): We got lucky and got in last minute because of a cancelation. The best tempura omakase experience we’ve had. Definitely try to get a reservation here or put yourself on the waitlist. (Has one Michelin Star)
Tempura Kondo (Ginza): Awesome omakase tempura experience. True story, Shinzo Abe and President Obama wanted to have dinner here, but Mr. Kondo wouldn’t cancel on his scheduled guests. BOSS. (Has two Michelin Stars)
Onodera Tempura (Multiple Locations): Great tempura experience, but I would prioritize getting into the two mentioned above.
Other:
Tousenkaku (Roppongi): Excellent Chinese food!! The sister restaurant has 3-Michelin Stars and is impossible to get into. I suggest doing the a la carte menu and sampling as much as possible. The Pecking duck is excellent. We’ve eaten here multiple times.
Sézanne (Marunouchi): This was voted the 2nd best restaurant in Asia, and I think it’s certainly on its way to graduating from 2 Michelin stars. Our dinner was flawless and one that I will remember forever! The interiors and art were perfect as well.
Kaikaya by the Sea (Shibuya): An AWESOME izakaya, and the food is outrageously good. You will need to have your hotel call to make a reservation and request to be seated in the non-smoking section — otherwise, your clothes may still smell like Kaikaya two years later. MUST ORDER TUNA SPARE RIBS.
Ginza Kojyu (Ginza): BE. PREPARED. This is a Kaiseki restaurant, aka Japanese Fine Dining, aka a four-hour 20+ course meal. If your visit to Japan is to celebrate something special, maybe consider eating here or if you want to experience a Kaiseki meal in general. But if you don’t have much time in Tokyo or feel jetlagged in the evening, skip it. The food was incredible, intricate (one course was made of gold), and memorable.
Restaurant Julia - Female chefs are still so rare in Japan, unfortunately. Chef Nao and her husband, the sommelier, only serve ten customers a night in their romantic restaurant. I loved this experience so much. It really felt like they were hosting you in their super stylish home. Watching them work independently and together was also very special. Fun fact: both of them trained at Gramercy Tavern.
Bars
Bartenders are no different from Chefs in Tokyo. Expect expertly-made cocktails and thoughtfully designed experiences wherever you go. Some bars do require reservations, so just double-check before you go.
Old Imperial Bar at The Imperial Hotel: One of our favorite bars in Tokyo. Originally designed by Frank Lloyd Wright, walking in kind of feels like going back in time. Perfect moody lighting.
Orchid Bar at The Okura (Toronoman): Another perfectly patinaed bar. The lobby of the Okura Hotel also feels like it’s frozen in time.
THESE Library Lounge (Roppongi): A little tricky to find, so keep an eye out and have Google Translate ready. They have a regular menu but will also make you a custom drink based on the fresh ingredients they have for that day.
Virtu at the Four Season Otemachi: Ranked one of the best bars in Asia and I would agree! Great views and expertly made cocktails.
Micro Bars (Golden Gai): Absolutely worth going to for the experience, so long as you’re not claustrophobic. Pick any bar that has enough open seats, has a clear fire exit, and doesn’t have a sign prohibiting tourists. Albatross is the bar that Anthony Bourdain visited in Parts Unknown.
NY Bar at the Park Hyatt (Shinjuku): If you can’t make it for brunch, have a drink and enjoy the live jazz.
Rooftop at the Andaz (Toranomon Hills): Amazing view and great cocktail selection.
Aman Tokyo: Great place for a nightcap. The bar/restaurant area is gorgeous.
Bars that have been recommended to us but we haven’t tried: Bar Trench, The SG Club, Memento Mori (get the cacao negroni), Ben Fiddich, Star Bar Ginza, and Bar Orchard Ginza.