The city, meanwhile, also is closing four East River bridges at 7 p.m. and they will remain closed until further notice, officials said. They are the Brooklyn, Manhattan, Williamsburg and Ed Koch Queensboro bridges.
Additionally, the city Transportation Department is closing the Joseph P. Addabbo Memorial Bridge in Queens, in coordination with the MTA's closure of the Cross Bay Bridge.
The bridges were closed as winds approached 60 mph. There are weather forecasts for gusts as high as 90 mph, Cuomo said.
Gov. Cuomo closed the Hugh Carey Tunnel (Brooklyn-Battery) and the Holland Tunnel closed at 2 p.m., and the Tappan Zee Bridge closed at4 p.m.
The Lincoln and Queens-Midtown Tunnels, remain open for now.
There was no traffic on the Bronx River Parkway.
Cuomo urged everyone to stay off the roads and stay indoors.
"Don't be fooled," he said. "The worst is still coming."
Kennedy LaGuardia and Newark airports are open, but all flights have been cancelled, the Port Authority said.
According to FlightAware, a flight tracking service, there are 7,118 flights cancelled in the U.S. Monday — 993 to or from Newark, 972 at Kennedy, and 918 at LaGuardia.
The MTA's two railroads — the largest in the country — are also shut down: Metro-North and the Long Island Rail Road.