Brooklyn will be your main port of call.
Queens (if your an old school run dmc fan). Staten Island (for Wu Tan Clan).
Basically depends what your into, though most of the hip-hop you are likley listening to will have originated from the 4 boroughs surrounding Manhattan.
However if you'd feel more comfortable stayin on Manhattan island, i've found Washington Square a cool place to hang out and watxh the basketball games and skaters (and listen to the occasional impromptu accapella).