I stayed at Homeikan but so you know that was three or four years ago. I thought it was quite nice for the price, the rooms were very large and I liked the breakfast. The neighborhood it is in is a charming area and there are lots of inexpensive places to eat nearby as it is so close to the University. I would stay there again.
I actually found it through this site:
Japanese Guest Houses - Japanese Inn (ryokan) Reservation Service