If you like ONE PIECE, there is ONE PIECE museum in 1st and 3rd floor of Tokyo Tower. There are exhibits and ONE PIECE themed restaurant, where you can enjoy cute dishes and delicious drinks supposed to be created by Sanji.
I found this article. Hope it helps!
Ghibli museum is famous.http://www.ghibli-museum.jp/en/
This site is list of manga's original picture exhibition.
(English of the site is Google translate)
Please be careful because there is an exhibition period.