The package was found shortly after 4 p.m. EDT (2000 GMT) in the baggage room area of Concourse B in Terminal 4, said Chris Valens, a spokesman for the Port Authority of New York and New Jersey.
After about 90 minutes, the terminal was re-opened.
The New York Police Department bomb squad determined that the package was a tube of toothpaste with duct tape around it, Officer James Duffy said.
"We determined that it only contained toothpaste," Duffy said.
The evacuation comes as the country is on edge following the Boston Marathon bombings and the discovery of letters laced with ricin, a highly lethal poison, addressed to President Barack Obama and Republican U.S. Senator Roger Wicker of Mississippi.
(Reporting by Jessica Toonkel; Editing by Stacey Joyce)