Kryzie King, 27, was arraigned Friday, two days after Myls Dobson was found malnourished and with severe burns on his body, CNN reported. She could face additional charges.
Emergency workers found the boy locked in a bathroom in King's apartment in a luxury building in the Hell's Kitchen neighborhood near Times Square.
Police Commissioner William Bratton said the young boy suffered "horrific injuries sustained over a period of days." Police reports say King admitted burning the boy, hitting him with a belt and locking him on a balcony dressed only in a T-shirt and shorts.
The boy's mother, Ashlee Dobson, lost custody in 2012 when she was living in a homeless shelter. WCBS-TV reported. His father asked King to take care of Myls when he was sent to jail in December on suspicion of bank fraud.
Dobson told reporters she had not seen her son since November, NY1 reported.
"I loved my son," she said. "He always loved me. He gave me kisses, like, 'Mommy, I love you.'"
A spokesman for Advocates Across Borders, Tony Herbert, blamed the city Administration for Children's Services for not ensuring Myls was in a safe place.
"You took the child from an atmosphere where he was protected, where he was safe, and then put him in a situation, what have you, where he's no longer here," Herbert said.