The city and its surroundings are seriously ginormous. Here are excellent places for taking it all in.

Shibuya Sky
Breathtaking rooftop experience on the 47th floor of the Scramble Square building in Shibuya. When clouds are not in the way, the view of Mount Fuji at sunset is stunning. The floor below has a viewing area, gallery, bar/lounge and souvenir shop. Reservation required and it is often necessary to book weeks in advance, but is worth it. (Shibuya Station on the JR Yamanote, Saikyo and Rinkai Lines or Narita Express, Tokyo Metro Ginza, Hanzomon, and Fukutoshin Lines, Tokyu Toyoko and Denentoshi Lines, Keio Inokashira Line, website, map)

Tokyo Sky Tree
Highest observation deck in Japan (Tokyo Sky Tree station on the Tobu Sky Tree Line or Oshiage station on the Hanzomon Line, website, map)

Tokyo Metropolitan Government Building
Free observation floor (Shinjuku Station on the JR Yamanote, Chuo, Sobu, Saikyo, Shonan-Shinjuku and Rinkai Lines or Narita Express, Odakyu Odawara Line, Keio Line, Tokyo Metro Marunouchi Line, Toei Oedo and Shinjuku Lines, website, map)