Cycling Terminals
Oddly enough, this cyclist has never stayed in a cycling terminal, but many people speak highly of them. At last count, there were about 50 nationwide, though they seem to be disappearing from some areas. Prices are quite low (about 5,000 yen a night including meals, which is less than most minshuku). Reportedly they have lots of information on cycling in the area. And, naturally, they have bicycles for rent, though these are likely to be very low-tech.
There is a list of cycling terminals in English, but no maps, at:
http://www.outdoorjapan.com/activities/cycling/activities-cycling-terminals.html
There is a much better list in Japanese at:
http://www.j-cycling.org/CYCLINGT/ct_area/index.html
Click on the name (not on the map) to display area maps with lists of terminals in that area; clicking on the name shows pages with the information about that terminal and nearby ones.
The cycling terminal association (Zenkoku Cycling Terminal Kyogikai) also puts out pamphlets listing the cycling terminals nationwide; if you're in Japan, send 200 yen in stamps to the JCA at the following address and they'll send you one.
Japan Cycling Association
Nihon Jitensha Kaikan No. 3
1-9-3 Akasaka, Minato-ku, Tokyo 107-0052
Tel 03-3583-5628
If you're not in Japan, you should probably contact them first to see if they'll mail overseas (and accept non-Japanese stamps or some other form of payment!).
For other reference materials that you may find useful in route planning, see RESOURCES.