Jeanine Cammarata, 37, a mother of three children and a substitute public school teacher in the city's borough of Staten Island, went missing on Saturday. Cammarata, who also worked at a Dollar Tree, didn't show up for work Monday.
Her disappearance sparked a desperate search by loved ones and police.
A body, described by Shea as "charred and unidentifiable," was discovered on Thursday at a storage facility on Staten Island. The New York City medical examiner performed an autopsy and made a positive identification Friday.
"This young woman has been positively identified as Jeanine Cammarata, with a positive identification made through dental records,” Chief Medical Examiner Dr. Barbara Sampson said in a statement.
The cause of death is pending, according to the medical examiner's office.
Her estranged husband, Michael Cammarata, was charged with second-degree murder on Friday, NYPD Chief of Detectives Dermot Shea said in on Twitter. Another suspect, Ayisha Egea, has also been charged with murder in the apparent death of Jeanine Cammarata.
"The investigation into the disappearance of Jeanine Cammarata is now officially a murder investigation," Shea tweeted. "Working closely with @StatenIslandDA, we have arrested Michael Cammarata & Ayisha Egea, both charged with Murder 2° #jeaninecammarata."
The suspects, who live in the same home in Queens, were also charged with concealment of a human corpse and tampering with physical evidence, according to the NYPD. Their relationship was not immediately clear.