The boy, identified as Ayden Wolfe, was found Saturday afternoon in the living room of his apartment on West 131st Street. Sources said he was covered in bruises and lacerations, old and new.
He was pronounced dead at Harlem Hospital.
His stepfather, 34-year-old Ryan Cato, was arrested and charged with murder and endangering the welfare of a child, CBS2's Nick Caloway reported.
"It's a tragedy through and through," neighbor Destiny Rogers said.
Rogers lives down the hall in the St. Nicholas Houses apartment building. Hours before police were called to the apartment, she said she heard what sounded like sporadic shouting. She was wearing headphones, so she didn't know which apartment it was coming from.
"I just raised my headphone really quickly, but I didn't hear anything that was alarming to me that would draw me to start worrying. Nothing at all. So just called the elevator and I walked out," Rogers said.
Advocates rallied outside the St. Nicholas Houses on Sunday afternoon, to pray for the little boy and stand against violence.
They said the city needs to invest and re-open community centers in all New York City Housing Authority facilities, so people who live there can have access to counselors.
"And be able to talk to somebody and say 'Miss Nina, I've got to talk to you.' And have that conversation. 'I'm being touched inappropriately, I'm not feeling comfortable.' Or whatever it is. We don't have those places," said Iesha Sekou, CEO and founder of Street Corner Resources.
"These walls are thin enough to where you can hear a child being beaten. You know what? You think it's not your business, but when it tragically winds up on the news, it is your business," added Tyrone Ball of the St. Nicholas Houses Tenant Association.
Some neighbors on the fourth floor are still shaken by the little boy's death. Rogers said she could barely sleep Saturday night, knowing what happened just down the hall.
"I never would have thought that something like that would hit close to home, because it seems like it's from a movie," Rogers said. "It's disgusting. It's just, it's just disgusting."
Police sources said the boy's mother was also being questioned.
CBS2 reached out to the Administration for Children's Services. A spokesperson said, "The safety and well being of New York City's children is our top priority. We are investigating this case with the NYPD."
CBS2's Nick Caloway contributed to this report
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