A person shooting photos discovered what looked like an arm on Thursday, said the official, who had direct knowledge of the case.
Police also found a torso and legs in the water, along with a dark-colored shoe and clothes resembling what the boy was last seen wearing, said the official, who was not authorized to speak publicly and spoke to The Associated Press on condition of anonymity.
Fourteen-year-old Avonte Oquendo has been missing since Oct. 4, the day he walked out of his school 4 toward a park overlooking the East River. His disappearance sparked a massive search that included hundreds of officers, marine units and volunteers.
Missing person posters were plastered on lampposts and placed on car windshields throughout the city. The teen, who did not speak, was fascinated with the subway system and Metropolitan Transportation Authority officials made announcements on trains for weeks asking for help finding him. Police checked every subway station and tunnel.
Authorities also hunted down hundreds of tips in New York City and suburbs. Despite a few false alarms, including an image of a person snapped on a train that resembled the boy, he has not been located.
But authorities are not clear whether the remains found Thursday belong to the missing teen. They were discovered at least 11 miles driving distance from his school.
The family's lawyer, David Perecman, said he spoke to Avonte's mother, Vanessa Fontaine, around 2 a.m. He said she was considering the discovery to be just another tip until she hears something more definitive.
The remains were removed to the Queens County Morgue and will be examined by the medical examiner's office to determine an identification and cause of death, and that may take several days, police said. Detectives and water units were at the site early Friday searching for any additional evidence.
A reward fund for information leading to Avonte's safe return was at least $60,000, including $50,000 from an anonymous donation to the advocacy group Autism Speaks.
Avonte's family has filed a notice of claim saying they planned to sue the city, arguing that the officials at Avonte's school allowed him to walk out of the building and waited too long to notify police that he was missing.
Associated Press writer Karen Matthews contributed to this report.