Investigators said police arrived at the hotel and found the boy, Jude Michael Mirra, dead on the bed.
His mother, Gigi Jordan, was sitting next to the bed with a faint pulse. She was taken to Bellevue Hospital.
There were prescription drugs found in the hotel room, investigators said. It's believed the boy died from an overdose, but the medical examiner will determine the cause of death.
Jordan did make statements implicating herself in the boy's death, police said, and it involved prescription drugs.
Investigators also found notes in the hotel room. One of them contained a password to a computer and read that if you wanted to know why to check her computer.
Authorities say Jordan was distraught over the end of her marriage and pending divorce.
She checked into the $600-a-night hotel room Wednesday. It is believed the boy was dead for about a day.
Police say they were contacted by the woman's relatives who feared the child was in danger. They first went to a luxury apartment complex near Central Park and then to the five-star Peninsula.
The Peninsula New York is at the Fifth Avenue and East 55th Street.