Google japanican...they've got some decent room rates if you don't mind staying in a "salaryman" hotel.

Depending how much commuting and snacking you want to do during the day, you can expect to spend about 7500 - 10000 yen per day, excluding accommodations. I was there last spring and was reminded how quickly the yen can disappear while you're enjoying yourself in Tokyo. If you want to travel on a tight budget, it is possible to have a good time to walk around Tokyo (my favorite thing to do) and it's very easy to find a meal for 800 yen or less.