Isaac Duran Infante, 23, of Bethlehem, Pennsylvania is charged with two counts each of first- and second-degree murder in the deaths of 32-year-old Felicia Barahona and her 4-year-old son, Miguel.
Their bodies were found in their Manhattan apartment Monday.
Felicia Barahona's body was found in the living room with an electrical cord wrapped around her neck, and Miguel was in the bathtub.
The building's superintendent spotted the garbage that Barahona had left sitting out since Friday and noticed that something was wrong.
"The superintendent smelled something no good in the apartment, and he called the police," neighbor Segundo Duenas said. "When the cops came, they opened the door, and they found her and the boy dead."
The medical examiner released the cause of death Tuesday after performing autopsies. Felicia Barahona died of ligature strangulation, and Miguel died of asphyxia due to neck compression. Their deaths were ruled homicides.
Law enforcement sources tell WABC that Infante confessed, initially blamed the devil for his gruesome actions. But he also reportedly told them he'd been angry about how Barahona had been parenting the child, particularly the clothes the boy was wearing. In an interview with WABC, Infante's brother-in-law said Barahona tightly controlled how much time Infante, who had bi-weekly visitation rights, could spend with his son.
"Miguel, he was cute, he was happy," Infante's brother-in-law said. "If he asked her, 'Oh, can I sleep with him today? I'll bring him to you tomorrow morning,' she said 'no, no, no, no, no.'"
It isn't clear what specifically set Infante off, but he had told his family he'd canceled a scheduled visit with his son over Christmas weekend. Sources believe both victims were likely already dead.
Barahona's family said there was a custody battle between the parents and that they had separated before Miguel was born.
Their son was conceived in a scandalous affair between Barahona, then a public school teacher in the Bronx, and Infante - her student at the time.
A 2013 report by school investigators determined the 36-year-old Barahona began a sexual relationship with Infante when he turned 18.
The report found Barahona believed she and Infante would get married before their relationship ended.
She was subsequently fired from the Bronx school.
"They kept in contact, I don't know how well," said Jaime Bravo, Barahona's brother. "They kept in contact, and I just know they actually did talk still, a little bit."
Family members said Infante had canceled a scheduled visit with his son this past weekend.
The family said Barahona was trying to turn her life around after her termination from the school district.