All we did in Montego Bay is fly in and get on a bus, but in Negril we stayed in a small, non-resort hotel and it was great. We spent a week in Negril, went all over (local restaurants, Rasta restaurants, local grocery store, etc.) and it was great-and safe. We spent one afternoon at a resort-it was so sanitized we couldn't stand it. Might as well have been at an amusement park.
Use common sense. Make friends with your hotel staff and use the taxis, etc. they reccommend. Our hotel had an (immaculate) Mazda 323 as their own taxi. I owned an earlier version of that car and made great friends with the driver/owner.
I've heard Kingston is very rough, and Montego Bay may be. But my experiences with the ordinary people of Negril is that they may not be rich, but they are some of the finest and most dignified people I ever had the pleasure to met. It amazed me to be up at 6 or 7 and see little kids waiting for school buses in neatly pressed and clean white shirts-outside of what most of us Americans would consider shacks.