Police say a custodian at a Queens church found the child after returning from lunch Monday afternoon.
Investigators say the baby was wrapped in towels and laying in the manger at the Holy Child of Jesus Church in Richmond Hill.
Police say the baby is in good health at a local hospital. Police have not released the gender.
State law says a newborn can be dropped off at a church, hospital, police or fire station. But it requires the child to be left with someone or for authorities to be called immediately.
A call to the church went unanswered Tuesday afternoon.