I have no idea what the "Flame war" posts were about but here are a few things you can try. I am a photographer but never printed anything in Tokyo, but have asked the same question to some fellow photographers in the past.
Nihon Hasshoku on Roppongi-dori, on the other side of the elevated highway from ANA Hotel and the Ark Hills building. I heard good things about these guys.
There is a Fuji Frontier lab near the Tameike-Sanno subway exit to ANA Hotel. From what I heard, their work is not as good as Nihon Hasshoku, but reasonable, and reasonably priced
Horiuchi Color has several locations and does good work
http://www.horiuchi-color.co.jp/index2/index2.html
You can also try National Photo in Harajuku. There is also a chain call Create, which has branches all over Tokyo
Good Luck!