Like Matt said, we went to St Bart's in July on a St Maarten stop day. We weren't confident with the reliability of the ferries (and it's a good thing because they didn't have one coming back in the afternoon on the day we were there) so we pre booked flights on WinAir out of SXM. Port time was 8-5 (all aboard at 4:30) and our flights were at 9:30 and 2:20 respectively. 15 min flight time.
First things first, you have to be ok with missing the ship and getting yourself to the next port. Start off your day knowing that. Everything went perfect for us until the flight back.