Here are some places you should try:
Mandarake in Akihabara and Nakano, the Nakano store is in a mall called Broadway (I believe) in it there are also some other toy stores. The one in Akihabara is a seven story building - it's called the Manadarake complex.
http://www.mandarake.co.jp/en/shop/
Yellow Submarine in Akihabara. It is near the train station in a six or seven story building. There are also some other stores there too.
There's also a toy store called Yamashiroya near Ueno Station, but they're also bit pricey.
Those are the main ones I can remember with Transformers, but in Akihabara there are a lot of little stores that sell all
sorts of toys you just need to go in and check.
Here is a link to HeroicDecepticons Blog, he goes in to some detail:
http://heroicdecepticon.blogspot.com...akano-and.html
Other places that might interest you include:
Hot Toys flagship store Toy Sapien near Harajuku Station:
http://www.toysapiens.jp/
Bandai Museum - I've never been there myself but you could try Googling.
EDIT: Forgot to mention Yodobashi Camera, that's the huge electronics store near Akihabara Station. They also have one near Ueno station, but smaller and with less selecton.
