We have used both Seaborne and Cape Air over the years. Cape Air many, many times to STT and VG and Seaborne once. We have also chartered 10+ times.
I like Cape Air. However, we have had enough of the afternoon delays out of SJU and Cape Air leaving bags behind due to weight restrictions. Carry-on only will eliminate some of the luggage issues but know they weight all bags.
Out of SJU, we have used Island Birds and Fly BVI. Great service from both.
From STT to SJU, we have used Air America (on Island Bird's recommendation), also great service.
Depending on how you are booking tickets, chartering can be equal to or slightly more than Cape Air/Seaborne without the hassle. At SJU, ground services transports your bags and escorts you directly to the plane.
If you have any questions, I am happy to help.