The district attorney's office said Shehada had allegedly threatened to kill his son, Amir, in the past because of his sexual orientation.
An investigation into who killed Issa's wife is still ongoing.
"The murder was committed because of the victim's sexual orientation and because of the defendant's perception of that status and the victims' association with a person and a group of that status," prosecutors said in a statement.
The son's body was found outside a North Hills house while Issa's wife was found stabbed to death inside the house.
Police said Issa told them that he had come home and found his wife's body in the bathroom. He said he shot his son in self-defense because the young man was threatening him with a knife.
According to Daily News, Detective John Doerbecker said:
"He claimed the son was armed with a knife, and there was no knife to be found there. It was a horrible family tragedy."
Issa is being held without bail pending his arraignment on April 11.
An investigation into who killed Issa's wife is still ongoing.