Besides booking directly via the accomodation's own website, there are websites available for Accomodation Reservations.

1. http://www.japanhotel.net/
   
   • I personally used this a few times, good rates and good service.
2. http://www.japaneseguesthouses.com/
   
   • This website specialise in Ryokans and minshuku bookings
3. http://travel.rakuten.co.jp/en/
   • Used once before, rates are pretty good.
4. http://www.itcj.jp/
5. http://www.itravel.jp/
6. http://www.jcha.or.jp/english
7. http://japanican.com/
8. http://www.ryokan.or.jp/index_en.html
   • This is a website where you can book ryokans part of the Japan Ryokan Association
9. http://www.jyh.or.jp/english/
   • This website specialise in Youth Hostels that are part of the Japan Youth Hostel group
10. http://www.hostel.com/
    • You can book minshukus, guest houses and hostels here

If you can read Japanese Jalan.net is a really good option.
In some instances it's cheaper (or equal to) than any hotel booking site in English and has a wider range of accomodations.