I've used Air BnB for accommodation while living in Japan and it was great, cheap and comfy.
I’ve heard a lot of good feedback from Air BnB, and my family and I use a flat rental service/company that’s similar to Air BnB whenever we go to england. I think since we’re going to be staying for around 12 days in Tokyo (with 2 full days in Tokyo Disney) it’s definitely a good option. Right now though we’re trying to get a rough estimate of costs for everything (airline, JR passes, museum passes, bus for going to airport on return flight, international phone setup, etc.) and seeing if my family’s amex agents and my own hotel rewards can help reduce costs. b/c we’re most likely only going to use the hotel to sleep for 7 hrs and drop off stuff when we get tired of carrying things around :P