I don't have recommendations for any of these cities,* but Trip Advisor is pretty good for first-hand accounts of specific lodgings. I used it on a trip to the UK and learned that a B&B that came highly recommended in Frommer's had changed hand and was now operated by someone who had no skills in either cleaning or cooking. (One bad review I take with a grain of salt. Consistent bad reviews mean something.)

*I take that back. I stayed in a nice budget ryokan in Nagoya, Ryokan Marutame, but it's not centrally located, hard to find, and non-English-speaking.