If you are spending your entire short trip in Tokyo, you have to remember that this city is huge, and it takes time to get from one end to the other. Plan your days so you cover the city neighborhood by neighborhood, coordinating sightseeing with dinner and evening plans. To help you get the most out of your stay, the suggested itineraries below will guide you to the most important attractions. Note, however, that some attractions are closed 1 day of the week, so plan your days accordingly. The itineraries start with one day in the city and adds one day at a time to help you get the most out of your stay.
If you have one day – Start by getting up in the wee hours of the morning (if you've just flown in from North America, you'll suffer from jet lag anyway and will be wide awake by 5 a.m.). Start by heading for the Tsukiji Fish Market, Japan's largest wholesale fish market (closed Sundays, holidays, and some Wednesdays). Be brave and try a breakfast of the freshest sushi you'll ever have. By 9 a.m. get on the Hibiya Line and get on your way to Ueno, where you'll head to the Tokyo National Museum, the country's largest and most important museum (closed Mon). From there, move on to Asakusa for lunch in one of the area's traditional Japanese restaurants, and follow it by a walk on Nakamise Dori (good for souvenirs) to Sensoji Temple. In the late afternoon you might want to head to Ginza for some shopping, followed by dinner in a restaurant of your choice. Drop by a yakitori-ya, a typical Japanese watering hole, for a drink and a snack. You might be exhausted by the end of the day, but you'll have seen some of the city's biggest highlights.
If you have two days – On the first day, get up early and go back to Tsukiji Fish Market. Next, head for the nearby Hama Rikyu Garden, which opens at 9 a.m.; it's about a 20-minute walk from Tsukiji, or a short taxi ride away. After touring the garden, one of the city's best, board the ferry that departs from inside the grounds for a trip up the Sumida River to Asakusa, where you can visit Sensoji Temple and shop along Nakamise Dori, following that with lunch in a traditional Japanese restaurant. Next, ride the bus to Ueno, where you should walk through Ueno Park to the Tokyo National Museum. Afterwards, head to Ginza's many department stores. If there's a performance, drop by the Kabukiza Theater for part of a Kabuki play. Have dinner at a Ginza restaurant.
On your second day, go early in the morning to the Edo-Tokyo Museum (located next to the sumo stadium), a great museum that illuminates the city's tumultuous history. From there, head to colorful Harajuku, where you can visit Meiji Jingu Shrine, Tokyo's most famous Shinto shrine; the Ota Memorial Museum of Art, with its collection of woodblock prints; and the Oriental Bazaar, a great place to shop for souvenirs. Spend the evening in one of Tokyo's famous nightlife districts, such as Shinjuku or Roppongi.
If you have three days – Spend the first two days as outlined above, and on the third day head for Kamakura, one of Japan's most important historical sites. Located an hour south of Tokyo by train, Kamakura served as the capital back in the 1100s and is packed with temples and shrines, one of which features the Great Buddha outdoor bronze statue.
If you have four days – Consider yourself lucky. Spend the first three days as outlined above; devote the fourth day to pursuing your own interests, such as taking a trip to one of Tokyo's numerous art or specialty museums, shopping, or soaking in a hot spring. This may be the evening to party, staying out until the first subways start running at 5 a.m.
If you have five days – You might visit Nikko, approximately two hours north of Tokyo, to see the sumptuous mausoleum of Tokugawa Ieyasu, the shogun who succeeded in unifying Japan in the 1600s. Or you might consider a 2-day trip to Hakone, famous for its fantastic open-air sculpture museum and home to some of the best old-fashioned Japanese inns near Tokyo. It also offers unparalleled views of Mount Fuji, if the weather is clear.
Source
http://www.frommers.com/destinations/japan/0229022927.html