A caretaker at a Queens church found the child, with the umbilical cord still attached, wrapped in towels in the manger after returning from lunch on Monday afternoon.
Queens District Attorney, Richard Brown, said the unidentified mother felt her new-born was in a warm place and would be found safe and the baby remains in good health despite being left in the Holy Child of Jesus Church in Richmond Hill for several hours.
The mother was located and interviewed about putting her son in a crèche at Holy Child of Jesus Church in Richmond Hill, Queens.
New York has a so-called 'safe haven' law, which means that new-born can be dropped off anonymously at a church, hospital, police or fire station without fear of prosecution.
However another law, known as the Abandoned Infant Protection Act, states that the child be left with a person or the person leaving the child to call authorities immediately.
Police said that did not happen in this case, which led investigators to begin searching for the mother.
Richard Brown said the mother followed the spirit of the Safe Haven law and therefore charges would not be brought: "It appears that the mother, in this case, felt her new-born child would be found safely in the church and chose to place the baby in the manger because it was the warmest place in the church, and further she returned the following morning to make certain that the baby had been found."