Patrick Gallagher, 50, a 17-year employee of the auction firm, was charged with grand larceny and criminal possession of stolen property, made up of 35 items he reportedly was going to sell for as little as $5,000.
Among them was the 1963 Father's day card the 2-year-old made for his father the year he was later assassinated.
There was also a letter from Queen Elizabeth II to President and Jacqueline Kennedy, congratulating them on the birth of their son.
All the items were recovered, and one law enforcement official estimated their collective value at more than $100,000.
Prosecutor Rachel Ferrari claimed at Gallagher's arraignment he stole the goods to pay off a bookie.
He is being held in lieu of $5,000 bond, the newspaper said.