The issue with St. Thomas is the return portion of the trip...

Flying into to St. Thomas (in my opinion) is great. We have a place there so have flown in and out many times. Even with the COVID protocols and checked bags it has always been stress free and pretty fast to get from the plane to the car. Once you are on St. Thomas there are lots of options to get to the BVI. Although there aren't many flights to grab and they are expensive, you can get a flight over to Beef Island. Better yet, you can go over by water taxi or ferry. I always recommend to fly in the day before, spend the night at an inexpensive hotel (Windward Passage is close and easy) and take the first ferry in the morning or arrange a water taxi.

Coming back from BVI is another story... First, you have to clear in when you arrive on either water taxi or ferry (not sure about flying in from EIS as I've never done that). Water taxi makes this much easier than the ferry. With the ferry you could end up in a long line depending on how many people are on the ferry and where you are in that line. Then you jump in a cab to go to the airport. The St. Thomas airport can be a total nightmare for how long it takes to get through checking in/bag tag/customs/TSA. The line (especially for American) to tag your bags can be outrageous and then you have to get in a line to go through customs/immigration again, even though you just did it on arrival by sea. Once through that you drop your bag and then get in another line for TSA.

For the reasons above I would book my trip to the BVI in one way sections. For the trip there I would fly into St. Thomas, stay at a hotel and then ferry over the next day (if you have more than 5 people I would book a water taxi). For the return trip I would fly out of EIS through San Juan.