We vacationed there over Thanksgiving, and it was fantastic! There's lots of ways to get there, almost all through SJU, including UAIR, NWA from DTW on Saturdays only, CAL from NY, and all the others mentioned.
I had no problems jumpseating AA from MIA-SJU-STX then back on UAIR to SJU and NW to DTW to go to work. We had no problems that were crime related whatsoever and wandered wherever, whenever. STX is trying to secede (sp?) from the U.S. and there is some friction there, so wouldn't be surprised about the unfriendly military response, but got nothing but friendliness from everyone else. They WANT tourists - it's just about their only trade.
Horseback riding was good, scuba off the north end is the BEST. If you take your own basic equipment, only $20 per dive for tank and weights and a guide - one guide for just you or you and your party - no crowded dive boats! Lots of octupi of many different varieties I'd never seen. Food was good but pricey - we FedEx'd a bunch of basic dried stuff down and cooked in the kitchen in our room on the cheap. Several good restaurants for "splurging".
Hope you have a great time!