Yet yacht-shuttles are also carrying boats to the South Pacific, and remote parts of Asia and Latin America. The services allow boat owners to fly in, use their boats and then have them transported to their next location. Industry executives estimate that more than 4,000 yachts will be transported by boat this year.
(Read More: Dan Loeb Gets $7 Million Break on Sandy Weill Yacht)
"For a lot of owners, time is of the essence," said Catalina Bujor, spokesperson for Dockwise Yacht Transport, the largest of the yacht transporters. Dockwise also runs a "yacht shuttle" between Newport, Rhode Island and St. Thomas.
Yacht transporters say that in addition to saving time, yacht-shipping allows owners to avoid the wear and tear that can come with an ocean voyage. After long ocean trips, boats can often require re-painting and repairs. Most yacht-shippers allow one passenger—sometimes the yacht captain—to accompany their boats on the voyage.
Dockwise recently introduced its latest yacht-carrying mega-ship, called Yacht Express. It can carry more than a dozen boats, depending on their size. The largest yacht Dockwise has shipped was over 200-feet long. But many of the boats it carries are smaller sailboats, sport-fishing boats and leisure cruisers.
(Read More: Billionaire Malone on Wealth, Death and Yachts)
The Yacht Express and other yacht-carriers are semi-submersible, which means the ship's cargo bay fills with water to allow the boats to pull into the ship. Once they're loaded and fastened, the water is drained for the ocean voyage. The process is reversed when the ships get to their destination.
Shipping a yacht isn't cheap. The cost of shipping a 120-foot yacht would be about $175,000, according to Dockwise.
Dockwise shipped about 600 boats last year and expects similar numbers this year. The yacht industry is still struggling from an over-supply of yachts for sale and charter, with prices still down 30 percent or more from the pre-crisis peak.
Yet for yacht-shippers, demand continues to slowly rebound.
"We've managed to do well despite the economy," Bujor said.
(Read More: Highlights From the 2013 New York Boat Show)
How the Yacht Express Works: