We usually leave the moorings base 2 hours before our flight. This gets us there about 1.5 hours before the flight. That's on Cape Air though, not sure if you need a little more time for Seaborne.

As far as connecting in San Juan, we usually have about 2 hours. We fly Jet Blue and Cape Air, so it will differ, but we have in the past had to exit security and go back through - this may have changed? Typically doesn't end up being a big deal though, although we do have TSA Pre-Check - sometimes I have had to go get our tickets re-printed in San Juan though as that doesn't appear when we get them in Tortola.

With 3 hours though, you'll have plenty of time.