I was just in Tokyo. I visited a few photo exhibits, but none were galleries selling prints.
here are a couple of notes:
lunch at megutama photobook cafe was kind of fun
http://megutama.com/en/what-is-megutama/
I almost walked right pas this place, did not immediately recognize from the web site photos.
They have an English menu
photo gallery (I did not make it here)
http://gallery916.com/access/
totem pole photo gallery (did not make it here either)
http://tppg.jp/about/aboutthegallery.html
Tokyo Metro Photo Museum -- Hiroshi Sugimoto exhibit and new photography exhibit
Most of the Sugimoto exhibit is not strongly photographic, but still very interesting
much info in English here
enjoy your trip!