Take the subway to Asakusa station and spend a few hours walking around.
This is one of the old parts of town that wasn't destroyed in WWII, it's filled with temples, markets and amazing architecture.
Go to the top of Tokyo Tower late in the afternoon and stay to see the city at night.
Don't listen to anyone who tells you how expensive food in Tokyo is. That's only if you order steaks from room service at your hotel. If you eat what the locals eat you'll get much better and more nourishing food for less money than any big city I can think of. Check out the Ramen noodle carts, the sushi at the convenience stores, the little cafes that sell gyoza and yakisoba.