Police Harbor Units and the FDNY searched for the man who went overboard Thursday night.
It happened just north of the Statue of Liberty around 10:30 p.m. as the ferry was heading from Manhattan to Staten Island.
The boat stopped for a half hour while a search by police and emergency workers got underway.
Helicopters were in the air aiding in the search.
The Coast Guard searched through the night before suspending efforts Friday morning.