Charlie Samuels, who was with the team 27 seasons, was awaiting arraignment on the charges, which also included tax fraud and falsifying business records. His attorney was in court and not immediately available for comment.
Samuels, 53, also worked as the team's equipment manager and traveling secretary and had unique and unfettered access to Mets equipment, authorities said.
Samuels stockpiled 507 signed and unsigned jerseys, 304 hats, 828 bats, 22 batting helmets and 10 equipment bags, valued together at more than $2.3 million, Queens District Attorney Richard Brown said.
Officials recovered the collectibles at a friend's basement in Madison, Conn. A commemorative Mets World Champions workout jersey signed by the entire 1986 team and a jersey made after the 9/11 attacks were each worth $7,500.
Prosecutors did not charge Samuels with selling the memorabilia.
"He was holding onto it as his own private collection so he could one day sell it," Brown said.
Samuels was fired in November amid claims that he placed bets on games and used Mets checks to cover his debts. The team said in a statement that Samuels was fired following an internal investigation that uncovered policy violations.
"We cooperated fully with the NYPD and the Queens District Attorney's office in their lengthy and thorough criminal investigation," the team said in a statement. "As this is a pending criminal matter, we will have no further comment."
Part of Samuels' job included signing off on meal expenses submitted by the umpire room manager, and he was also accused of padding expenses, then skimming the excess to receive an extra $24,955 in reimbursement from 2007 through 2010. He was also accused of failing to report on his tax returns $203,780 in dues and gratuities he'd received from ball players over the years.
"The defendant had a dream job that any Mets fan would die for - and he blew it," Brown said. "His greed is alleged to have gotten the better of him."
Samuels began his career with the National League team in 1976.
He was made equipment manager in 1983 and later took on the other responsibilities.
If convicted of the top charge of first-degree criminal possession of stolen property, he could face between eight and 25 years in prison.
The investigation was conducted by the New York Police Department's organized crime division.