There are very few places where you can hire decent bikes here in Japan.
A couple of downhill orientated places within reach of Tokyo, which do offer bike hire are Fujimi Panorama
http://www.fujimipanorama.com/summer/index.php
and Mt. Takamineyama
http://www.takamineyama.com/english%20page.htm
Fujimi is a ski area in Winter with MTB access in Summer only. Uplift by cablecar with 3 courses coming back down. A course is a big, fast, old-school type DH race course. B course is steep and technical. C course is listed as a "beginner" course but is actually pretty serious and you can hit very high speed on it.
Takamineyama is a dedicated MTB place. It's off the beaten track; if you do go then get the owners to pick you up from the station. Uplift is by van with bikes in the back. There are 3 main courses and 2 that head down the back side of the mountain and involve some pedalling to get back to base. The trails are woody, singletrack descents off the top of the mountain. They have some jumps and wooden skinnies too. I really like the riding there.
Plan on spending about 8000 Yen per day including the bike hire at either location and bring cash since they don't take credit cards.