Sixteen-year-old Marcell Dockery pleaded not guilty to murder charges.
His attorney, Jesse Young, says Dockery denies he confessed to setting the fire and wants to call an expert to back his claims.
"The statements made are adamantly denied by my client," Young said.
Officer Dennis Guerra died in the April 6 blaze, and his partner, Officer Rosa Rodriguez, was hospitalized in critical condition.
Police claim Dockery admitted to detectives that he was simply bored when he set fire to a mattress in the 13th floor of the Unity Towers housing project.
Rodriguez and Guerra were the first to respond and were overcome by smoke the instant they stepped out of the elevator.
Dockery had already been charged with arson and reckless endangerment. Guerra's death led prosecutors to seek a murder indictment.
"Both dedicated and courageous officers did not hesitate to risk their lives to save others," Kings County District Attorney Kenneth P. Thompson said. "We will bring the defendant to justice for these terrible and horrific crimes."