We've done both. In all honesty, I think it's a toss up. STT is cheaper, but then you've got to pay for the ferry. Also, some of the inbound flights to STT cut it pretty close on getting the last ferry of the day, so you might have to spend the night in St. Thomas. Not that that's necessarily a bad thing--any excuse for a meal at Cuzzin's is a good thing in my book. You've got a lot more flight choices into STT. For EIS, you're pretty much going through San Juan or Antigua.
I suspect I will alternate, just to be different. If it were my first trip, I'd pick STT or EIS based on which flights worked better for my schedule. I've generally sailed with The Moorings in Roadtown, which is marginally closer to EIS than Soper's Hole. If you are chartering from someone closer to the west end of Tortola, then STT and a ferry is a pretty clear win.
If you do go the STT route, pay attention to where the ferrys are starting and ending. On our last Moorings sail, we got a ferry from Charlotte Amalie direct to Roadtown. CA is only about 15 minutes from the airport. If you leave from Red Hook, you've got a pretty long taxi ride to the ferry terminal. On the Tortola side, Soper's Hole is not so convenient if you are sailing out of Roadtown, but great for points west.
If you take a ferry from CA, there's a very good bar/restaurant upstairs at the CA ferry terminal. Their Ginger Beer is home made and unfiltered, so If you are into that, I highly recommend one--or even better, a Dark and Stormy.
One final tidbit: We had to wait in a pretty long line for C&E at the Roadtown ferry dock last time. In the sun.