The only ferry to the Virgin Islands [1] departs from Fajardo, Puerto Rico [2], once a week. Transportation Services of St. John (340/776-6282, $60 one-way, $100 round-trip) runs the ferry, which departs Fajardo on Sundays at 1 p.m. It leaves St. John [3] on Fridays at 7 a.m. and St. Thomas [4] on Fridays at 7:30 a.m. Advance reservations are required. The journey takes two hours, and you ride in relative comfort in a large double-decker boat able to seat some 250 people (it is never that crowded). If you are susceptible to seasickness, take precautions such as seasickness tables.
Links:
[1] http://www.moon.com/destinations/virgin-islands/discover-the-virgin-islands
[2] http://www.moon.com/destinations/puerto-rico/east-coast/fajardo
[3] http://www.moon.com/destinations/virgin-islands/st-john
[4] http://www.moon.com/destinations/virgin-islands/st-thomas