Observation Decks

The following observation decks cost money

http://www.japan-guide.com/e/e3057.html

Tokyo Sky tree: 2060 yen, 350 meters,  Asakusa

Sunshine 60, 620 yen, 226 meters,  Ikebukuro

Mori Tower: 1800 yen, 52 floors, 218 meters,  Roppongi

World Trade Center: 620 yen - 500 yen with coupon, 40 floors, 152 meters, Hamamatsucho 

Tokyo Tower: 820 yen, 150 meters, Minato

The following observation decks are free

http://supermerlion.com/10-free-tokyo-city-views/

Metro Govt Buildings, free, 45 floors, 202 meters,  Shinjuku

Bunkyo Civic Center, free, 25 floors, 130 meters, Bunkyo