Oquendo's mother was notified early Tuesday afternoon, officials said, and the family's attorney said she was inconsolable. The cause and manner of death are pending.
"She finally just broke down," David Perecman said of his phone call to her. He said it was the first time except for brief moments that he'd seen her cry that much.
Perecman said the family intends to file a wrongful death lawsuit against the city, alleging that school officials failed to monitor the boy or call the police quickly enough when he left the school.
"Now that the inevitable, unfortunately, has occurred, undoubtedly she'll go through a metamorphosis of a sort, and I'm sure she'll get good and angry," he said.
Perecman says he will file the legal claim on behalf of the family. Avonte's remains were found at the edge of the East River last week.
"There were so many things that went wrong, it befuddles the mind," he said.
Carmen Farina, the city's newly appointed education chancellor, said she was heartbroken.
"There's no way to explain to a mother what happened. I actually sent her a personal note. I don't want to intrude on them. I think they have to handler this as a family issue. But certainly our hope is to do whatever we have to do so this doesn't happen again. And we learn from these kinds of issues. But there's nothing I can say that's going to make this better."
A teenager shooting photos for a school project noticed the arm on the riverbank last week. Police then found the lower part of a torso and legs on the rocks at low tide, along with black Air Jordan sneakers, white socks and tattered denim jeans. A part of a skull and teeth were recovered a few days later.
For weeks, family, friends and strangers searched for Avonte. His missing poster was plastered in the subways, poles and windshields as part of the all-out effort to find him.
The teen, who was non-verbal, 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.
One investigative theory was that Avonte might have tumbled into the river near the park, though his family has said he was fearful of water.
The body parts were found at least 11 miles from where he was last seen. Though the remains were found upriver, past densely-populated shoreline and the Rikers Island jail, the East River is a tidal strait with strong currents that reverse flow many times a day.