If you ever feel like seeing Tokyo from above, why don’t you go to the Tokyo Metropolitan Office Building in Shinjuku (Tokyo To-cho 東京都庁). Its two towers are open to the public, and it is possible to go up to the highest level (45th floor) for free.
You will be able to see Tokyo if the sky is clear (if you are luckier than me) and you may even be able to see the Mount Fuji!
Enjoy!