But the boy did not have smoke or soot in his mouth or airway, which would have indicated he had been alive when the fire broke out, said officials.
A 911 caller reported the Franklins' 457 State Route 8 home in Mount Upton, a hamlet of Guilford, was on fire around 1:15 a.m. on March 1.
When police arrived on the scene, Ernest Franklin reportedly pointed to the room where his dead son was lying.
Mr Franklin, 35, said he had been outside chasing his dogs when the fire occurred. The mother told authorities she had been running errands until 2:30 a.m. when she returned home to find the house in flames.
"She inexplicably left the house, driving around Chenango County and Delaware County, and doesn't return until the fire totally engulfs the house", McBride said. "Because of the damage to the body by the fire, the pathologist is not able to determine the cause of death", the attorney said.
Heather Franklin's attorney, Michael Trosset, told the court that she's "innocent until proven guilty".
According to a transcript of a Friday bail review obtained by local station WBNG, Chenango County District Attorney Joseph McBride alleged that on the night of the murder, Heather Franklin watched the Oscar-nominated movie, Manchester by the Sea, in which the main character, played by Casey Affleck, kills his children in an accidental fire. The movie scored two Oscars from six nominations, including a best actor win for Affleck.
Ernest and Heather Franklin have been charged with murder, arson, and tampering with evidence.
Casey Affleck, victor of Best Actor for Manchester by the Sea, holds his Oscar at the 89th Academy Awards in Hollywood, California on February 26, 2017. Neither had posted bail Wednesday.
This story has been corrected to show Affleck portrayed the father, not the uncle, of the children who died in the fire.
Heather and Ernest Franklin were indicted on March 24 on charges of second-degree murder, according to the Chenango County Sheriff's Office in NY.
A couple accused of murdering their disabled adopted son are said to have been inspired by a major plot point in Kenneth Lonergan's Oscar-winning Manchester by the Sea in their ensuing attempt at covering it up, according to their case's prosecutor.
Ernest Franklin's bail was set at $250,000 and his wife's at $125,000. Ernest and Heather Franklin chose to kill their disabled adoptive son and cover up the crime with a house fire after watching the Oscar-winning movie "Manchester by the Sea", according to the NY prosecutor handling the case.