Wilbert Cortez, 49, who taught at P.S. 174 (William Sydney Mount School), faces several charges including first-degree sexual abuse and endangering the welfare of a child, according to the office of Queens District Attorney Richard A. Brown.
"These are serious accusations in which a school teacher — who should serve as a role model to students — is instead accused of using his position to gain access to children for his own gratification," Brown said in a statement.
"Schools should be safe havens where students are protected from harm."
Officials said Cortez molested two boys, ages 6 and 10, in his classroom between 2007 and 2011. He allegedly abused a third boy, who was 8 years old, in the teachers' bathroom, according to prosecutors.
He was already charged with fondling two students through their clothing between Sept. 7, 2010 and June 30, 2011.
Cortez, who was reassigned out of the classroom last year, is free on $50,000 bail and faces seven years in prison if convicted.