Isales and the matron, 38-year-old Ruth Thames, face endangering welfare of a child charges.
Neither he nor the matron noticed the two-year-old was inside the bus.
Several hours later, a man walking his dog heard crying coming from the bus.
He went to the nearby Jim Thorpe School and got a school security agent.
The boy, two-year-old Aiden Long, was found inside. He was crying and had dirtied his diaper, but was otherwise ok.
He was taken to Coney Island Hospital to be checked out.
The boy was supposed to attend Infant and Child Learning Center in Brooklyn.