The armada was overseen by former fire commissioner Thomas Von Essen, who lost 343 firefighters in the terrorist attack on the World Trade Center.
He called the "Sail for America" event another step forward for "a country, a city and a people who have begun to heal."
In what was billed as New York's symbolic rebirth, flotillas of boats converged in the harbor after sailing from the East River, the George Washington Bridge and the Verrazano Narrows Bridge.
Aboard the boats, more than 3,000 memorial flags were flown - each bearing the name of a victim from the terrorist attacks in New York, Washington and Pennsylvania. The flags will eventually be presented to the victims' families.
The flags were the idea of Cathy DeRubbio, whose brother-in-law David died on Sept. 11.
"The families have called me, blessed me, cried," she said. "Sailing is soothing."
Also on Saturday, hikers planned to place American flags at the top of New Hampshire's 48 peaks that are taller than 4,000 feet elevation. Hikers were to leave the banners flying for 2 hours, then bring them down again.
Basil Dixon, a native of Britain who became a U.S. citizen about five years ago, flew a kite shaped like an American flag from the summit of Mount Lincoln, elevation 5,089 feet. Dixon, of Boston, later flew the kite from nearby Mount Lafayette, elevation 5,260 feet.
"After 9-11, even though it was a global event, it was kind of poignant to carry an American flag up with friends and know that many of these peaks also were going to have flags," he said.