At those airports, the metropolitan area's third major airport in Newark, New Jersey, and Boston's Logan International Airport, as many as three out of four flights were called off, according to tracking service FlightAware.com.
Temperatures were expected to verge on minus 20 degrees Celsius in many areas of the northeastern United States late on Friday and into Saturday, with some more northerly states, such as ME and New Hampshire, seeing the mercury plummet to minus 40 degrees Celsius, the National Weather Service said.
Almost 500 members of the National Guard were activated along the East Coast to assist with emergency response, including 200 in NY state, the US Department of Defense said in a statement.
In Connecticut, where the storm is expected to hit Thursday, Gov. Dan Malloy urged motorists to stay off roads.
After bringing rare snowfall to the southeast a day earlier, the storm carried rapid accumulation and high winds to NY, where subway systems appeared less crowded than usual as many commuters heeded officials' warnings to stay home.
Thousands of flights were canceled, snow plows and salt trucks rumbled along roads and highways, and New York City's two main airports halted flights due to whiteout conditions. A half foot of snow was on the ground as of noon, local time.
"With this forecast in mind, all Virginians should take the necessary precautions now to ensure they are prepared for the travel disruptions, power outages and other threats to health and safety that could arise during this significant weather event".
As forecast, temperatures plunged on Friday - despite sunny conditions, they were not expected to rise above 12 degrees Fahrenheit (minus 11 Celsius) in NY and Boston.
NY sanitation workers are getting ready to deploy 2,200 ploughs to help clear the streets, City's Sanitation Commissioner Kathryn Garcia, said.
Boston could see minus 7 degree temperatures paired with about 12 inches of snow, forecasters say.
Massachusetts Gov. Charlie Baker said the greatest areas of concern are along the Plymouth County coast, from Sandwich to Dennis on Cape Cod.
On Wednesday, the same storm brought historic cities in the Southeastern United States their heaviest snowfall in three decades.
Cities in the Southeast that rarely see snow turned into winter wonderlands as dozens of vehicle crashes were reported and airports closed.
A blizzard warning means severe winter weather conditions are expected or occurring. Charleston, South Carolina, received 5.3 inches of accumulation, within an inch of its record.
The cold also raised the risk that road salt would not work to melt ice, possibly leaving highway crews to shift over to sanding roads to improve traction, MA transportation officials said.
Amid the Instagram-worthy scenes, McMaster warned of unsafe conditions as evening temperatures were expected to remain below freezing through Monday.
Bomb cyclones can draw colder air in from the north, then blast out icy temperatures.
"With continued frigid temperatures expected to last for several more days, road conditions will remain treacherous beyond the expected end of the snowfall today", he added.