Zamperoni never re-emerged from the room.
He had been reported missing by his colleagues when he failed to show for work at the upscale restaurant.
The chef, who was originally from Italy, had also missed his weekly call with his mother.
The criminal complaint says Barini is also linked to the deaths of two other men, including one found dead at the Airway Inn at LaGuardia on July 4 and the July 11 death of a man at the Crown Motor Inn in Woodside.
She is accused of working with drug dealers to sometimes rob customers after they are drugged and incapacitated.
Authorities say surveillance video showed her with the two other men at the respective hotels.