Jeanine Cammarata, 37, was last seen near Denker Place and McVeigh Avenue around 9 p.m. Saturday when she left her current boyfriend's house.
The remains were found inside a storage facility in the Arden Heights section. Police are working to identify the remains.
NYPD has surveillance video showing her estranged husband, 42-year-old Michael Cammarata, leaving his Far Rockaway, Queens apartment building with a bag. Surveillance video at the storage facility has what appears to be the same man entering with the same bag.
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NYPD obtained a search warrant and found the yet-to-be-identified body.
"If in fact, the father did something nefarious, then the children may have lost both a mother and a father and the trauma to them is going to be tremendous," said Eric Gansberg, Jeanine's attorney.
Cammarata, has been in custody since Tuesday and is currently charged with assault. The charge is for allegedly hitting Jeanine in the past.
The two reportedly have a tumultuous relationship with prior domestic incident reports filed, and they are said to be in the process of divorce, with an ongoing child custody battle in the court. Friends say Jeanine was terrified of Michael.
"I believe he probably beat her, because she was afraid of him," Gansberg said. "She was terrified of him."
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"Harassment, following her in the car," landlord Jose Perez said. "She even escalated it because she was concerned about her safety. And I mentioned it to her, I said to her, 'You better get this thing straightened out because you don't want any problems' ... She always texted me where she's at or if something's happening to her. But she has not."
Michael Cammarata is charged with assault as the investigation continues into his wife's disappearance.
Perez, her landlord and former co-worker, has known the couple for years. He last saw Jeanine two weeks ago.
"He wasn't giving her her kids, she wasn't able to see her kids, and that's when she said, 'OK, I had enough. I'm gonna go get a lawyer, I'm gonna get divorced, and I'm gonna get custody of my kids,'" Perez said. "And now she's gone."
Cammarata was charged after he allegedly confessed to hitting Jeanine in the past, but detectives have not connected him to her disappearance, at least not publicly.
She did not show up to work Monday or Tuesday at PS 29 on Staten Island. She also has a second job at a Dollar Tree on Staten Island.
"She let me know Friday she was going to go pick up her children Saturday," said Elizabeth Torres, who works at the Dollar Tree.
The boyfriend called 911 Saturday and said Cammarata was gone, last seen leaving his New Springville apartment to meet her estranged husband and see their kids.
"That's the last anybody actually saw her," said Jessica Pobega, Cammarata's best friend.
Authorities are looking into text messages received by Pobega from someone claiming to be Cammarata the day after she disappeared.
Pobega wrote in the texts that she was calling the police.
"I don't want that," the reply read. "I have the kids ... I apologize. I have to do this for the children."
Cammarata also did not show up for a custody hearing in court this week.
Police say another friend got a text allegedly from Cammarata, saying she just wanted to get away.
"She didn't see the children this weekend, so I don't know who that was and what they were covering for," Pobega said. "She's my oldest friend. My mother is distraught. Something happened. Something bad happened. And I don't know what it is, and I really hope I'm wrong."
Anyone with information in regard to this incident is asked to call the NYPD's Crime Stoppers Hotline at 1-800-577-TIPS (8477) or for Spanish, 1-888-57-PISTA (74782).