We flew out of Isla Grande, which is a separate airport in San Juan, on Vieques Air Link. We arrived into SJU around noon, went into Old San Juan, got lunch, walked around, saw the fort, then took a 10 minute cab ride to Isla Grande for the flight at 4:30. The flights out of Isla Grande are MUCH cheaper than out of SJU. The downside is that if your flight into SJU gets delayed you could have a problem rebooking the second flight because they are separate tickets, so I would allow a buffer between the flights.