The most recommended observatory in Tokyo
Tokyo Metropolitan Government Office (Japanese website only)
The government office in west Shinjuku has observation rooms on the 45th floor (202m), which are open until 23:00 on most days.
This place is not as famouse as Tokyo Tower as an observation platform to view the whole panorama of Tokyo, but is usually most recommended by Sakura staff.
Reason 1: Admission free!!
Reason 2: It's even higher than the main observatory of Tokyo Tower.
Reason 3: Not that famous yet, which means that not so many tourists yet.
During the winter season when we have a clear sky, you might be able to see Mt. Fuji from there. And, of couse, the night view is something that you shouldn't miss while in Tokyo.
The photos I took with my camera were disappointing... So these are photos by somebody else.
Ah, I should go to Akihabara to buy a better camera...