• I want to know the hidden spots not in a travel guide book!

I really like museums, traditional/historical places, and very peaceful-not crowded areas.

I've been to some of the other "big" places in Tokyo, like Meji Shrine and Asakusa, so I want to try to see some "smaller" areas the next time I am in Tokyo.

Well, did you try Kamakura 鎌倉? And how about Sakura 佐倉 in Chiba? There is National Museum of Japanese History and small but nice historical area. About the museum, check out this link.
http://www.rekihaku.ac.jp/

代官山(Daikanyama) and 恵比寿(Ebisu) are really calm and peaceful places. :)

I recommend Omoide yokocho(思い出横丁) in Shinjuku. This place is a nostalgic and rustic street not in a package tour. There are a lot of small Izakaya(Japanese style pub). You can eat Japanese food which local people like, for example Yakitori(roast chicken), Soba, Sushi. If you go upstairs at some Izakaya, you might sit down on Tatami(Japanese traditional mat).

Hey Grace! I really recommend you visit the museum, "デザインあ展" in Roppongi! My friends are always talking about this and it seems so interesting... :D

http://design-ah.net/

Chika, thank you so much! I will go there soon! (it looks really interesting)

Thank you everyone for the interesting answers!