The 25-year-old woman, whom has been identified by NBC New York as Latisha Fisher, took her 20-month-old son Gavriel into the toilets of a Boro Burger at around 2.25pm.
Inside the toilets, she was reportedly spotted by another woman.
However she did not stop what she was doing, saying simply: "I put my hand over his mouth to put him to sleep."
The mother eventually wound up locking herself and her son in the bathroom - and customers and workers soon became worried.
But, by the time they forced their way inside, the child was reportedly already unconscious and foaming at the mouth.
Fisher apparently tried to stop restaurant staff from performing CPR on her son, later saying that she “blamed the devil for what she did”.
Gavriel was rushed to Bellevue Hospital, where he died, police have said.
The mother, whom has been described as “soulless” by law enforcement officials, has been taken into custody.
Speaking with local news channels after the tragedy, the woman’s mother insisted: “It’s hard, it’s really unbelievable. I know my daughter loved her son.
“He was such a happy baby.”