Cos-play is at Harajuku on sundays, get there early maybe about 11-12 am.
Also walk toward the meiji shrine if you go there and turn left after the bridge where cos-play is on, keep walking on the sidewalk until you see the group of elvis guys dancing around... that is pretty weird stuff.
Tons of stuff in Tokyo, depends what you want to shoot. Often times you can get great shots by shooting stuff on the street (people, etc..). If you get an early morning, go to Tsukiji fish market at tsukiji station for crazy stuff (fish auctions...).
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.