Vieques has an airport--pretty nice now (compared to when I went many moons ago) We used the local airline, which I believe flies from both airports now (Is the old domestic one still in op?) It was Vieques AirLink and had weight restrictions!
You can also take a bus from the airport to Fajardo then the ferry. The island is pretty cool! The Bioluminescent Bay is NOT to be missed if you go.