The plane was quarantined at JFK airport as those on board were checked by health officials. Eleven went to hospital but others declined treatment.
The US Centers for Disease Control and Prevention (CDC) said that initially about 100 people including some crew had complained of illness.
Flight 203 from Dubai landed at 09:10 (13.10 GMT) with 521 passengers.
Emergency vehicles were seen on the runway as it landed.
In a statement, the CDC said: "Approximately 100 passengers, including some crew on the flight, complained of illness including cough, fever, and symptoms of gastrointestinal illness.
It said that after completing health evaluations on everyone on board, 538 passengers had been released and 11 people were taken to a local hospital for care.
"Passengers who have been evaluated and released [should] call their provider and health department if they develop any symptoms," the health body advised.
A spokesman for New York's mayor, Bill de Blasio, said that some of the passengers had originally come from the Saudi Arabian city of Mecca, which was currently experiencing a flu outbreak, and that the passengers' symptoms were "pointing to the flu".