We stayed at the Ryokan Shigetsu in Asakusa about 4 years ago. Our room was a kind of two-room suite with four futons on tatamis in one room and sliding doors that connected to a sitting area in the other. It wasn't huge, but served us well. Tokyo rooms tend to be small compared to the US.
While more of a "ryokan-hotel" rather than a real ryokan, the Shigetsu we found offered a very nice experience in a colorful part of Tokyo, right off the pedestrian shopping stalls leading to Sensoji temple. There is a hot bath with a view of the temple from the top floor.
I believe they may have western rooms as well, since you asked about a queen bed.