I think this question always boils down to time and money. What is more important to you? We have done both ways and always find flying into Beef a little more expensive but usually a better experience regarding getting to the boat and even getting away from the dock the same day on occasion.

-Most places from the US, you have cheaper flights to SJU and more options but then you have the logistics of missing flights if your flight is late and you book separately with Seaborne or Cape Air to Beef. That is less of a problem if you book via one airline as I think American has a partnership with one of them.

There are private charters such as Fly BVI who will meet you when your plane lands and take you straight to Beef from either SJU or STT if money is not an issue and you want the quickest experience. We have done this several times and love it but can't always justify the expense. But it is oh so nice to walk off your plane and have them get your luggage and take it to their plane and be headed to Tortola in less than 45 minutes of arrival to SJU. You get a nice panoramic view of the islands too. We do this from STT sometimes as well.

-Flying into STT gives you more options with public ferry, private water taxi, and private air charter but typically less flights to choose from and more expensive flights in our experience. If you get a comparably priced flight between STT and SJU, then I would choose STT every time due to proximity and options personally. We have had good experience both with private ferry and public ferry.

Having said that, we are taking a late flight into SJU in February, staying overnight and taking the first Seaborne flight at 07:00 the next morning to Beef so we can get provisioned and get off the dock that afternoon. The rest of my crew is coming in later that day to STT and taking a private water taxi to meet us at JVD. Bottom line is find what works best for you and crew regarding the balance of timing and expense. That has been different for us on every trip.

Oh and I don't think you have much stress with your option of STT and private water taxi. I think that may be the best option as the water taxi can be scheduled to your private group and really lessens the concerns for logistics in my mind.