Maybe this list is of help to you:

http://japaneseguesthouses.com/hotspring.htm

If going to Kyoto there is the famed Kurama Onsen in the mountains just North of the city. Unfortunately, they only have same - sex baths, but the scenery and food is quite nice. They can be found at:

http://japaneseguesthouses.com/db/kyoto/kurama.htm

or their Japanese homepage:

http://www.kurama-onsen.co.jp/