The driver, who was found later in Brooklyn, wasn't hurt, police and FedEx Corp. spokesman Steve Barber said.
The truck — an 18-wheeler and one of the biggest FedEx vehicles — was later found abandoned in the Williamsburg section of Brooklyn around 5:30 a.m. There was cargo inside, officials said.
"We don't know whether anything is missing at this point," said Sandra Munoz, a FedEx spokeswoman at the company's headquarters in Memphis, Tenn.
The FedEx Express truck was headed to a company facility in Newark, N.J., after midnight when two men brandishing a gun confronted the driver at a traffic light, police said. The driver was forced out of the truck and into a car. He was found at about 1:30 a.m. in Brooklyn, police said.
Munoz said FedEx could not estimate the value of the cargo until police released the truck, which can hold as much as 80,000 pounds when full.