I've tried Sakura House and
Villa Saranda.
I like Villa Saranda better, although it is a sharehouse it prefers long term tenants but the manager is pretty easy to talk to.
What I liked about Sakura House is the free events for foreigners. I got 2 free tickets from them to an expensive Koto Performance , so it was a nice experience.
There are lots of sharehouses in Tokyo, but these two are the ones that I've stayed with.