i'd recomend getting a JR (japan rail) pass, i'm pretty sure travel agencies are the only people that can hook you up with those, i forgot how much they cost but you get unlimited rides on JR lines, including a bunch of lines in tokyo, i think any and all shinkansen (bullet trains), in smaller cities like hiroshima the trams, and some ferries are operated by JR, so get one cause they come in handy.
besides whats been mentioned, near Ueno station in Tokyo, theres a bunch of shops with shutter fronts under the tracks, and a few have nice legal pieces on the fronts of them, so check that place out after everyone's closed up shop. i also saw some nice stuff on the walls along the east side of the Sumida river.
theres stuff everywhere, just gotta keep your eyes peeled. but i'm sure you know all about that. have a good trip.