There are loads of places:
Akihabara, loads of cheap electronics and a few anime stores. Just wander around. Try and go to a maid cafe.
Shinjuku, few places but Akihabara is better
Before you go look at: http://www.mandarake.co.jp/english/shop/
Print out the maps, the Nakano store is a bit of a trek but has loads of shops with older kits. If you are looking at getting modern kits then you can't go wrong with Akihabara.