The plane was later moved to an American Airlines hangar.
WSOC learned the Port Authority of New York is taking the lead on the investigation because they don't know if the incident happened in the air or when the plane landed.
According to WABC, the teen, who did not alert the plane's crew, was admitted to the hospital after the flight.
The Queens District Attorney's Office will determine whether charges will be filed.
The medical examiner's office is checking to see how the baby died, but said that the baby had a gestational age of 5 months, CNN reported.
At a gestational age of 5 months, which is part of the second trimester, a fetus would have the look of a newborn, but would not normally be able to live outside the womb, according to the American Pregnancy Association.
A spokesperson with American Airlines issued the following statement:
"As we continue to learn more about this tragic and sensitive situation, we are working actively with law enforcement on the investigation. Please contact law enforcement for additional information."
The Cox Media Group National Content Desk contributed to this report.