1) Shibuya for all the babes
2) Shinijuku, Kabukicho for the night life (be careful of snapping pics of guys dressed in suits approaching girls, they are most likely unsavoury characters and might take offence at being snapped)
3) Asakusa, Sensoji Temple. A Japanese Temple and landmark
4) Tsukiji Market (Must go from 5am to 8am, after 9am, the main market closes)
5) Ginza, lots of sights and some iconic buildings like Sony showroom
6) Harajuku and Otemosando (Iconic buildings like Prada building)
Advice, Bring telephoto lenses, you can snap at people from afar. Some japanese do resent being snap up close like a subject.