I checked out a few photo galleries when I was in Tokyo, and my favorite by far was Totem Pole, in Shinjuku. There was an excellent exhibition up called "Blazing Heat" by Sekiguchi Naoki, who I think is also a part-proprietor of the gallery. I can't say for sure, but judging from the website it seems that Totem Pole is run by a strong group of photographers who regularly exhibit work. The work is of a very high quality, I would certainly make a point to visit again. Here are some of my favorites from what's on their site.
The current exhibition is of Fukuyama Emi, it goes up today but closes in just two weeks! Looks like is standard practice for Tokyo exhibits, you've got to act fast to catch stuff I guess. If you're going to be in Tokyo sometime and want to check it out, be sure to look at its entry on Tokyo Art Beat. It's in English, will tell you what's on display and also link to excellent maps which you must print out if you actually want to find it.