Emergency crews rushed the boy, identified as Justin Stephens, to Community Hospital, where doctors pronounced him dead.
Police initially responded to the scene in Flatbush following a 911 call for an emotionally disturbed person.
Authorities say it appears the mother left a suicide note and tried to jump off a balcony, but a Good Samaritan intervened and notified police.
Now, 20-year-old Anna Thomas is facing murder and manslaughter charges .
An autopsy being conducted by the Medical Examiner will determine the cause of death. There were no signs of trauma.
When police responded to Thomas' home, they observed her attempting to jump out a window.
Thomas is a nurse. She was staying at her aunt's house.