If you're a foodie, you can head to the Mandarin Oriental Hotel in Tokyo. K'Shiki has an incredible breakfast buffet that starts from 6am, and the view of Tokyo from the 36th floor is most impressive. I believe it was 2800 yen plus service charge for the basic deal, which is actually quite reasonable for the quality of the food.

http://www.mandarinoriental.com/tokyo/dining/kshiki/

The lobby bathroom is also an attraction in itself. You'll know it when you see it!