Do visit a depachika, the epicurean food floors in the basement of major department stores. My favorites are Takashimaya (both in Nihonbashi and Shinjuku), Isetan in Shinjuku, Mitsukoshi in Ginza, Tokyu Toyokoten in Shibuya, and Tobu in Ikebukuro. An incredible variety of food is exquisitely presented. In particular, be sure to check out the wagashi (Japanese confectionaries) that are edible works of art. If you are hungry, grab a seat at one of the eat-in counters or head to the restaurant floor in the department store. If you are riding the bullet train (shinkansen) then give yourself time to pick up a bento from Daimaru’s depachika at Tokyo station. The sake department also sells small bottles of nihonshu or beer if you would like to have these with your bento. Be sure to ask for some plastic cups. Wait to eat your bento until the train has started moving. You’ll notice your fellow travelers doing the same.
Do go to the New York Bar and Grill. Made famous from Sofia Coppola’s Lost in Translation. Either have a drink at the bar while the sun is setting and watch the lights come up on the city, or splurge for lunch or dinner. Lunch there is a great buffet of appetizers and desserts while you select your main course. Dinner is a real treat with the city sparkling below you.
Do have sushi at Tsukiji Market. I suggest visiting the outer market. If you insist on going to the inner market, it is best to visit after 9 a.m. and to stay out of the way of the fishmongers as this is their workplace. Most of the Japanese follow these same rules. While here, do have breakfast or lunch, sushi if you are game, if not, plenty of great cooked food as well. Try Sushi Bun or Nakaya for sushi or Tenfusa for tempura of shrimp or anago (eel).
Do try the local sake (nihonshu), shochu, or even the local wine. A visit to Tokyo would not be complete without some local drinks, be it nihonshu, shochu, or the local koshu wine. I like the izakaya, Yamariki in Morishita, as it is where many locals go. It is famous for its nikomi, simmered innards and grilled meats. For wine lovers with time to venture out of the city, consider a day trip to Coco Farm and Winery, just north of Tokyo. There is a tasting room as well as a café overlooking the vineyards. It is open all year long.
Do try as many foods as you can, and be adventurous. If you are willing to try foods you have never had before, you are in for a treat. As an island, Japanese has amazing seafood, much of it never exported so be sure to try seasonal sushi if you can. If you like innards be sure to go to Saiseisakaba in Shinjuku, a standing bar that does amazing raw and grilled innards – perfect with some shochu. If you can, try shirako, sperm sac from fish, notably from the fugu (blowfish) or ankimo (monkfish liver), which is like foie gras of the sea.
Do splurge and have a kaiseki meal. Seasonal cuisine served in courses is a treat. My favorite restaurant for this is Nihonbashi Yukari. I believe dinner starts at about 10,500 Japanese yen. If you are on a budget, go for lunch and request the Yukari bento when you make your reservation (it must be ordered in advance) (about 3,675 Japanese yen). The bento is not kaiseki, but does include several different components of kaiseki in a large bento box. Chef Kimio Nonaga was the 2002 Iron Chef champion. He is very talented and passionate about Japanese cuisine. If you get a seat at the counter you can watch him at work. Tell him Yukari sent you.
Try exploring some of the older neighborhoods of Tokyo like Nihonbashi, Ningyocho, or Asakusa. The charm of these areas can be felt in some of the historic restaurants, some going back several generations, like Tamahide in Ningyocho.
Do whet your appetite for your trip by seeing some great movies like Lost in Translation and Tampopo. If you are into ramen, then check out Ivan Ramen, some of the best ramen in the city made by a New Yorker.
Do try other cuisines than Japanese if your schedule permits it. Japanese chefs do an amazing job with French and Chinese cuisine. In particular, Italian food done with Japanese ingredients is a match made in heaven.
Do plan ahead and do your research. Don’t miss the last train, don’t take a taxi from Narita to the city, don’t travel during rush hour, don’t book a meal at a restaurant that only has seating on the floor unless you are comfortable sitting that way. Try avoid your travel during the major holidays of obon, Golden Week, and New Year’s as many restaurants and Tsukiji Market will close. If you are in the city while a sumo tournament is going on, then do try to see this sporting event live. Summer can be unbearably hot and humid, in particular late July and August. Ideally, come during the cherry blossom season in the spring or in the fall to witness the colorful leaves.