Highly recommend Hakone Ginyu for a ryokan experience. We went in the winter and the climate was perfect for an experience like that. Spring or summer may be too hot. November would be nice.
For airbnb we stayed at:
Osaka:
https://www.airbnb.ca/rooms/4813116
and
https://www.airbnb.ca/rooms/3929000
Both are a lot roomier than other places I staying in Japan.
In Tokyo, they've all been tiny cramped units and i couldnt really recommend any.
We stayed here:
https://www.airbnb.ca/rooms/3530743
and it was convenient as it was a 2 min walk from Meguro station on the Yamanote line.