You may find public transport limiting. Kawaguchi-ko is the best connected of the lakes. So you might choose to stay close to there.

Here's a ranking of minshuku in the area:
http://www.jalan.net/ranking/minshuku/LRG_150600.html

Bear in mind that anyone who has renewed an ordinary Japanese driver's license in the last couple of years is allowed to drive a small bus with up to 29 seats. It may be worth considering renting a large vehicle from a place in Kofu (or Otsuki) IMHO. That will open up more possibilities in terms of locations you can visit and places you can easily stay.