Sorry for digging up an old thread, but I've been busy the past few months -- 1 April I started a new job as lead brewer for Baird Brewing Co here in Japan. I'm down in Numazu, Shizuoka (just had a major 6.5 earthquake today) at our brewery, but we have two pub restaurants in Tokyo that might be worth checking out. One is in Nakameguro (called Nakameguro Taproom) -- it's on the map linked above. There are ~30 taps there plus three handpumps, although there's usually only two handpump beers on at any time. Our other pub is in Harajuku and just opened last weekend (also on the link above). Those two only serve our beer, but we put out nine regular beers and countless seasonals, so you should be able to find something you like.
Besides that, some of my favorite places in Tokyo are Popeye, The Aldgate, Ushitora -- all worth checking out, especially Popeye if you have limited time. There are also a bunch of places in Yokohama that I haven't personally been to, but everybody raves about them -- especially Thrash Zone and Craft Beer Bar. There are more, but those are the places I'm familiar with.
One correction of some information above -- Baird's Fishmarket Taproom isn't in Tokyo, it's in front of the Fishmarket in our home base of Numazu, Shizuoka, about 1.5 hours from Tokyo to the southwest. If any of you do make the trip down here, please let me know -- I'll meet up with you at Fishmarket Taproom, give you a brewery tour if you're into that kind of thing, and maybe even buy you a pint.
Chris, Lead Brewer, Baird Brewing