So, due to the fact that there are 3 of us, and hotels with 2 double beds are almost nonexistent, we settled on an apartment.
Entire Apartment - Roppongi: Has Wi-Fi and Balcony - TripAdvisor

Hell of a deal too, 550 for 4 nights wtf!! Kitchen, etc. I'll update when we return. Btw, this is Golden Week in Tokyo, no wonder I had such a hard time finding accomodations for the weekend!