I dunno, I went indie-gamedev a few months ago and I've done nearly all my work in St. Marcs, Ueshimas, Tullys, Forests and so forth. Most have power outlets in at least some seats, and on weekdays they never really get crowded enough to care about space (at least not where I am a few minutes outside of Shibuya). The downside is wifi, but the fact that I work better without it is half the reason I'm at a cafe!

With that said for non-chain places with wifi, Streamer Cafe was a short walk from Nakameguro and was a nice place to spend an afternoon. Timeout cafe (Ebisu above liquid room) was reasonable as well, modulo a sales guy using it for an office.

Would be great to sponge a lunch off you someday ;)