Costas,
There are shops all over the place, and yes the prices are better than online, unfortunatly I live 60- 80 km form the Tokyo and only know the local shops in my area and I had to find those by looking for them while driving around. But, there are 2 in Tokyo that I know of both are in Akiabara the Electronics Shopping District. One is rather obscure and on the 5 th florr of a building in the middle of the district (its marked on the guide map) call Yellow Submarine, they specialize in Figure and obsure japanese subjects in resin. the other is by the train staion at the west end of the district its also marked on the map. But they sell eveything and its several floors of Hobby items. Now, a question for you are you coming as well???? If so take a bullet down to Shizuoka and take a free shuttle to the Hobby show in 2 weeks. There will be vendors from all the Major Japanese companies and you can easily spend a lot of money, but you'll get twice as much stuff than going to any local shop in Japan. HTH STUG