There is a good website I use that lists many free and cheap campsites as well as rider houses all over Japan - http://www.hatinosu.net. It's in Japanese but you can use the map to locate the campsites. I've referred to this website a few times when camping around Hokuriku and Shikoku, it's great. I plan to use it to find campsites in Kanto region too.
I've also found some articles on camping in Japan from the JapanTravel website which have been helpful. Enjoy.