I was about to ask you if you had been to the Tamiya shop in Shimbashi, but just found out that there's another one in Yokohama. It's inside the Tressa Yokohama mall (http://www.tressa-yokohama.jp/access/googlemap
) . The Tamiya Plamodel Factory is run by Tamiya so it only carrys Tamiya kits, but you will find all the products on the Tamiya catalog and that includes Tamiya novelties that you won't find in other places (shirts, ties, pens, etc.) . They also have "factory" space where you can build the kits.
As for other places in Tokyo, I really can't think of a "you can't miss" place since so many places have gone out of business in the last 10 years or so. Some places I personally go to in Tokyo are
Dora: Odakyu Line / Tokyo Metro Yoyogi Hachiman Station about 3 minutes. Across from the post office. Google map 35.668136,139.690282
This is a tiny shop but it's been around forever and carries strictly scale kits only. http://gdora.web.fc2.com/index.html
Sunny: Odakyu Line / Keio Inokashira Line Shimokitazawa Station. Google map 35.660783,139.668267
This place is a bit hard to find in the very crowded Shimokitazawa zone, but has a pretty good selection. Shimokitazawa itself is a very interesting shopping / culture zone. http://www.hobbyshop-sunny.co.jp/
Nakama Mokei Center: JR Chuo Line, Nishi Ogikubo Station Google map 35.704269,139.602864 .
Another old shop since 1965. Interesting because they sell collections consigned by customers, i.e. old kits that's been sitting in someone's closet. Sometimes you find that rare kit for a good price. Another good thing is, the shop is open until 10PM on weekdays and Sundays, and until 11PM on Friday and Saturday nights. http://www.omohan.com/shops/view/256
Kiya Hobby: Chuo Line, Ogikubo Station (next to the station above) in the Town 7 building in front of the north exit. http://kiyahobby.co.jp/k/index.php?main_page=page_2
Yamashiroya: Across the street from the Hirokoji exit of Ueno Station. http://www.e-yamashiroya.com/
This is a large toyshop with a floor for plastic kits. If you are using the Ueno Station to travel elsewhere, this is a nice place to kill time.
I can go on.
So what do you build? I build (uh, I haven't completed anything in 3 years ...) but I mainly do aircraft. The last thing I built was the vintage Monogram Wright cyclone engine. See http://plamo-net.com/search.php?id=jetawabi&genre=item