[godwine]

Spend one day at the Daiba, don't take a train, get off at shinbashi station and switch to the local Tokyo Metro line, I don't remember the station name (if someone can help), but get off one station before you hit the rainbow bridge, walk across the brdige, which is the best thing to do to have a great view

Night life: Shinjuku and Shibuya

Shrine: Harajuku, there is also a nice temple in Kamakura, which is not far from Tokyo, also go to Asakusa for the Sensoji shrine

Entertainment: Ueno, Akiba area...

Allt hese should "cost" you about 3 days... the tokyo tower is one of those thing that you really want to go but will be a disappointment when you are up there....