Nytavia Ragsdale, 26, was charged with criminally negligent homicide and endangering the welfare of a child, according to police.
Ragsdale is slated to appear in criminal court on Tuesday.
Officers say they arrived at the scene on Adam Clayton Powell Boulevard just before 7:45 p.m. and found Jahmeik Modlin unconscious and unresponsive.
Modlin appeared to be malnourished and police initially thought his body was covered in burn marks but those marks were revealed to be eczema.
"My God. What kind of mess is going on?" said one resident. "It's hard. It hurts my heart."
Surveillance video from Sunday shows NYPD escorting Ragsdale from her Harlem apartment as she carried her son's body.
Neighbors say they never knew the woman had a son or saw the child.
"One of the biggest things this morning that broke my heart was that nobody knew that this woman had a child," said community advocate Iesha Sekou. "A child was attached to this woman. When you have a 4-year-old child, that child is usually outside playing, being mischievous, everybody knows the kid. Nobody knew a 4-year-old kid and even knew that she has a child?"
Ragsdale apparently has three other children who have since been placed in the care of relatives.
The Administration for Children's Services has previously investigated Ragsdale for malnourishment, but the agency was unable to substantiate the claims.
Luis Tavares -- the building super where Modlin was found -- says he's never heard any noise coming from the apartment. He added there were never any issues with the tenants.
The medical examiner will determine the cause of death.
ALSO READ | Community calls for postpartum care changes after mother dies weeks after giving birth
Vigil held for mom who died from embolism weeks after giving birth
----------
* Get Eyewitness News Delivered
* More Manhattan news
* Send us a news tip
* Download the abc7NY app for breaking news alerts
* Follow us on YouTube