St Thomas it almost always the better point to enter on a cost basis. Beef Island get you on Tortola faster but typically that is through
PR and you want to avoid that place if possible.
Problem with STT that time of years is that is outside the normal "Tourist" season and most Ferry's stop around 5. Best to arrange flights that will arrive at STT by 3:00. While the Ferry dock you will want is near by... delays in getting a taxi out is typical as they fill the vans to max capacity before they send them out. Make sure your driver knows WHICH Ferry dock your going to or you could end up in Red Hook.
If you do have to stay in St. Thomas overnight... take care. Many locations are less than safe including the area around the ferry docks in Charlotte Amalie. Some "resort" area may be safer and typically not much more expensive. You may even want to consider spending the night on St. John and take the morning ferry to either Road Town or West End.