The city-bound flight diverted to Scotland on Saturday landed at JFK Airport early Sunday morning, but not all passengers were aboard.
Scottish authorities say of the roughly 300 passengers aboard EgyptAir flight 985, five stayed in Great Britain to seek asylum.
The flight was diverted to Glasgow when someone found a letter in the bathroom threatening to blow up the plane.
British defense officials said they sent fighter jets to escort the flight.
At Glasgow, the passengers were taken off the plane while officials ran background checks and searched the plane.
The flight finally touched ground in New York after 4 a.m. Sunday. It was unclear if the plane that landed in New York was the same plane passengers originally boarded.
Passengers said they landed quickly but could not get off the plane for some time.
"To be sitting on the plane for four hours thinking at any given time the whole plane could blow up and not knowing whether or not, the first thing that one wants to do is get off the plane, but we couldn't get off the plane," said one passenger.
"First they said they had technical difficulties so we all got ready and landed quickly but snipers were the tip-off that this was not a technical problem," said another.
The flight was originally supposed to have arrived around 3:15 p.m. Saturday.