The victim's family confirmed later in the day that the remains belonged to their loved one, 13-year-old Garrett Warren.
Several people spotted the body near the Madison Avenue Bridge where it was recovered and brought to shore.
An autopsy is expected to be performed on Friday.
[Ads /]
The NYPD had asked for the public's help on Tuesday to help find 13-year-old Garrett Warren and 11-year-old Alfa Barrie.
Both boys were last spotted this weekend and were believed to have been seen together at a park near 143rd and Lenox.
The search continues for the missing 11-year-old and his family is holding out hope.
"Right now is a trying time for both families, we ask that you guys keep them both in your prayers, we need all prayers we can get," said Warren's godmother Christine Vargas.
Nothing was found in the immediate vicinity where Warren's body was located, but the NYPD's chopper was out searching, along with officers from the harbor unit.
[Ads /]
ALSO READ | Woman reported missing on Mother's Day found dead in Bayonne
Woman reported missing on Mother's Day found dead in Bayonne
----------
* Get Eyewitness News Delivered
* More New York City news
* Send us a news tip
* Download the abc7NY app for breaking news alerts
* Follow us on YouTube