Video from the scene showed only the hull of the small vessel visible above the water.
The Department of Homeland Security said Thursday their search of 850-foot Ville D’Aquarius was over.
The Coast Guard, law enforcement and other officials were inspecting the containers as part of the massive response. The ship can carry more than 2,000 cargo containers and the search could take all night, officials said.
The Coast Guard says experts are working to recover unexploded ammunition found last weekend under the Verrazano Narrows Bridge.