Sawanoya is a gem in quiet Yanaka, run by a very friendly family and with all the traditional hospitality you would expect of a ryokan. The shared cypress and earthenware baths are the perfect balm after a long day (a couple of slightly more expensive rooms have their own bath, too). The lobby overflows with information about travel options in Japan.
Bicycles are available for rent, and lion-dance performances are occasionally held for guests.