The Fukiji fish market is a fantastic place to photograph. You need to go really early to catch the action. Ask around, I don;t remember the best time but it's 5 AM or something like that (good for jet-lagged travelers who are up early anyway). You can also have breakfast at one of the small restaurants that cater to the workers.
Also, the Imperial Palace offers great gardens and architecture. The Ginza at night is fine if you like neon signs.