I'm late to the game on this thread but just an FYI- I would never rely on the ferry system as a tourist. It's bad even for residents and they get first dibs on tickets and tourists are turned away. I always fly from either SJU or ISG, which is only about 10-15 cab ride from SJU and the flights are only $75 each way.
If anyone ever has any questions, you can PM me. I lived their for almost 5 years and am back in the states currently. Also, Cape Air's service and cancellations have been horrible lately. Not worth the price. Go to Isla Grande airport and take a VAL flight.