According to local media reports, the vessel, which was carrying 27 people, hit the sandbar near Rockaway Point Boulevard and Beach 201st Street, authorities said.
No injuries have been reported.
New York's police, fire departments along with the Coast Guard have responded to the stuck ferry.
It is the second stranding in a month for the city's newly-expanded ferry service which was launched on May 1 and is operated by Hornblower.
On Nov 27, a Rockaway-bound ferry with 120 people and one dog got caught on a sandbar made of construction debris near Wall Street.