We haven't been in two years, but we went regularly before that. We went through St Thomas a couple of times and flew into Beef Island the rest. Given the two choices and costs to fly in not being too much more expensive, we always found flying in to be a better experience.
I have same question as OP, STT or EIS for a sail departing from Tortola. Matt, is the better experience due to the easier logistics? I'll have 2 less experienced travelers in tow so the easier it is to herd them about the better, even if the cost is somewhat more.
For us, there were always a few factors. First and foremost, I never found the ferry experience to be enjoyable. I think we took it two times and both times we came back on a Sunday and the music was blaring. Went outside to get away from it and it was just as bad if not worse. That may have changed or may have just been a sunday thing as it was church music.. The customs lines were always a pain though.
We have global entry, so flying in and out always seemed to be a better experience. No wait in customs on the return and arriving, especially on Cape air which is what we used the majority of the time, even customs on entry to EIS wasn't bad at all. Never minded have a couple hours in San Juan either since it always gave us time to eat. And prior to us travelling with my son (who turns 4 in Feb), we would even take some red eyes BOS-SJU and the first flight the next morning, making a noon start on a Saturday possible - not at all possible via STT.
Price however can be steep at times, so as much as we prefer to fly via EIS, we will look at the options via STT. I know last I checked, they were both fairly expensive and not a significant savings going via STT. Another bonus of the SJU to EIS flight - the views. I've got some amazing pictures from those flights.
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