NEW YORK – The man accused of killing a Queens imam and his associate faced a judge on Thursday as his defense attorney raised questions about the case.

Members of the Al-Furqan Jame Masjid mosque filled the courtroom as Oscar Morel, 35, entered a not guilty plea.

Morel is charged with one count of first-degree murder, two counts of second-degree murder and two counts of second-degree criminal possession of a weapon in the shooting deaths of Imam Maulana Alauddin Akonjee and Thara Uddin.

“They find the gun, what else you need?” one man said.

But Morel’s defense attorney, Michael Schwed, said his client maintains his innocence and questioned how the gun got into the apartment.

“They say it was found in his house,” he said. “I haven’t seen any proof of that yet.”

He also said witnesses failed to pick him out of a lineup.

“In fact, one person picked out another individual in that lineup,” he said. “I’m not just making that up. The DA put that on the record.”

He said while his client didn’t do it, the person who did it had a motive.

“Has nothing to do with religion or hate crimes,” he said. “It has to do somewhat with the mosque itself not particularly liking the imam.”

Mosque members disputed that claim, saying he was well-liked and well respected.

Akonjee and Uddin were walking home from the mosque on Aug. 13 when police said Morel came up from behind at the intersection of 79th Street and Liberty Avenue and fired multiple rounds, shooting both victims in the head. They were taken to the hospital where they were pronounced dead.

Police said Morel was seen on surveillance video fleeing the area of the shooting in a black GMC Trailblazer. About 10 minutes later, a car matching that description struck a bicyclist nearby in Brooklyn, police said.

Morel was later taken into custody outside a Brooklyn apartment as he approached the vehicle that police had linked to the hit-and-run, authorities said.

Police said they recovered a revolver at his Brooklyn home and clothes similar to those worn by the suspect  in the surveillance video.

While many in the community have called on the shooting to be investigated as a hate crime, authorities said the alleged motive remains unclear.

If convicted, Morel faces up to life in prison without the possibility of parole.