I was lucky enough to live in Tokyo for a year and see a lot of shows.
54-71 - Genius band, mentioned before by origin98. Very weird, and the vocals are off-putting at first. Imagine if US Maple was a hip-hop band (if you can). Last two records recorded by Bob Weston at Electrical ("enclorox") and Soma ("men of non-doing"). I didn't get it until I saw them live. Drummer plays off to the side, bass player stands in the back facing the stage wall. Guitarist's name is "scumgrinder".
Gaji - Monotone female vocals with a Jesus Lizard-style rythym section and noisy guitar work. Guitarist is in the band Thermo.
Thermo - Two person band consisting of the original Melt Banana drummer whose drums are miked and then electronically manipulated by second member. The only output from the band going to the house PA is the electronics. This is a genius idea that will be stolen continuously. Maybe by me.
Boris - Mentioned by everyone. At best when they were trying to recreate Melvin's "Lysol" on the "Amplifier Worship" record. "Heavy Rocks" is also good. Best song is on the Inoxia Record's "From Koenji to Eternity" comp. HUGE guitar sound made by a small woman named Wata playing through four Orange 4x12 cabs.
Kirihito - Another two person band, guitar and drums only. Drummer plays standing up with no bass drum. Guitar tone is manipulated to sound like a synth. They put small crappy keyboards at the front of the stage and step on them once in awhile to make some piercing noise.
Boris, Gaji, Kirihito, and Thermo records can all be ordered from Inoxia Records. The dollar is weak so obviously you'll pay out the ass.
http://www.inoxia-rec.com/