There are loads and are one of THE reasons to go to Japan!
Hakkone or Izu near Tokyo can be done easily as overnight trips. Check my blog for details.
The alps have loads if you go hiking - try Akadake for example.
Or if you head south, Beppu on Kyushu is famed for boiling Onsen. If you can get down this far, try Sakkurajima which has an Onsen with a volcano on one side and then ocean on the other. (see my flickr stream for pictures)
Enjoy about 7 years ago