This from New York 1 as of 10:40 am:

Transit officials urged New Yorkers to delay their morning commute
after severe weather flooded numerous subway stations and roads
throughout the area, leading to massive mass transit delays during the
morning rush.

NYC Transit spokesman Paul Fleuranges says the subway system could
not handle the morning rush, and that he guesses it will take at least
until noon or later to get all of the system back up and running
normally.

"No subway line right now that is running at full normal of its
route, so if people are at home, they’re about to leave their house,
advice to you is don’t,” said Fleuranges. “If you can delay your
commute, if you can go in a little later, do so cause right now we
probably can’t handle you and we probably can’t get you from point A to
point B."

As of 10 a.m. there was no service at all on the L, 3, V, W, and G
trains. Also in Brooklyn little or no service on the 2, the F, the B/Q,
or the N, which was not running Manhattan-bound between Coney Island
and 36th Strett.

In Queens, there was no E train service.

Also in Manhattan, there was no 1 train below 14th Street, and no trains in Manhattan on the 4/5/6 line.

As of 10 a.m., limited service had been restored on the Port
Washington Branch on one of the two tracks with residual delays of 30
minutes. Earlier, service was suspended due to flooding conditions at
Bayside. The railroad also said it was experiencing 25 to 30 minute
delays systemwide as a result weather related flooding in several
locations.

Just before 9 a.m., MetroNorth reported that all service –
northbound and southbound – has been restored on the Hudson, Harlem and
New Haven Lines through the Mott Haven area. All service is operating
through the area slowly and customers will be significantly delayed.

Reports of storm damage are coming in from all around the boroughs.

A heavy storm with tornado-like winds ripped the roofs off several
houses in the Bay Ridge section of Brooklyn, damaging several houses
and downing a number of trees.

Flatbush residents also reported damaged houses and crushed cars along several blocks.

Power outages were also reported on Staten Island as a result of flooding.

The storms prompted the National Weather Service to issue a tornado
warning for Staten Island, Brooklyn and Queens shortly before 6:30 a.m.
The warning expired at 7:15 a.m