Tokyo Metropolitan Gov't Building Observatory is a real time commitment — fit it in only if it's a priority.
Allow 45 min–1 hr.
It's free, central in Shinjuku, and on a clear day you get a vast city panorama with Fuji on the horizon — unbeatable value. The trade-off versus the paid decks: it's lower, viewed through windows, and the deck plus the new nightly projection-mapping show can mean a queue.