The 3:40 arrival is easy to catch a ferry out of CA. If the flight runs late in my experience the last ferry will always wait. Since the flight will be taking off 4 hours before it arrives it's easy to know if it will be on time. Check the status right after departure time. If the flight is running to late to make a ferry then it's easy to audible at that point and head up to STT.
A big factor would be how many days is the charter. If it's a seven day charter the ferry option would be my first choice hands down. If it's a 10 day charter with a sleepaboard I would consider the STT pickup.
Keep in mind to go and pick them up you have to deal with customs 3 different times. Out of the BVI, into the USVI and back into the BVI.
One last point. If there is a North Swell running then the North Shore anchorages for St Johns will not be a good option.
G