The painting was valued at $2.5 million in 2001, but is believed to be worth much more now.
Customs officials weren't fooled and turned over the small painting to homeland security agents who invited French art experts to examine it at the Long Island City facility.
Brigitte Leal, Deputy Director of Collections at Musee Nationale d'Art Moderne, and Veronique Serano-Steadman, head curator at the museum, inspected the canvas and determined it was actually the multi-million dollar masterpiece.
"A lost treasure has been found," said U.S. Attorney Lynch of the move to seize the piece and return it to France. "Because of the blatant smuggling in this case the painting is subject to forfeiture to the United States. Forfeiture of the painting will extract it from the grasp of the black market in stolen art so it can be returned to its rightful owner," Lynch said.
U.S. and French authorities have not announced any arrests in the case.
Pompidou director Alain Seban said the discovery comes as a "true comfort" at a time when the cultural world is reeling from an Islamic State video showing the destruction of statues in Iraq.
Seban said in a statement Friday that he hopes the work can be exhibited again publicly in May.
The Associated Press contributed to this report.