I use Cape Air. Mainly because they have a 10 ticket commuter book that locks in that price. I also love the small aircraft and views you get from it. They also have a decent number of flight options which helps too.

For us, going to Tortola via SJU gets us in at the beginning of day 1 instead of the end and allows us to leave mid day the last day instead of first thing. This gives us 2 extra nights in an anchorage. Clearly its more expensive, but given what we get its worth the extra cost.

So my advice - look a the cost (don't forget to look at all of them - ferry, extra taxi..etc) and consider what other benefits there may be. For some this means STT is better, but I think a lot of people over look SJU.