The third suspect, who was not identified Tuesday, was expected to surrender on Thursday for arraignment before a Suffolk County Court judge, said Robert Clifford, a spokesman for District Attorney Thomas Spota.
Justin Higgins, 21, and Nashon Minter, 19, both of Mastic, each pleaded not guilty to charges of second-degree gang assault, assault as a hate crime and assault.
Each was held on $25,000 cash bail.
Assistant District Attorney Patricia Brosco said in court that Minter said he would "beat the gay" as he and Higgins attacked Dixon at the Mastic Beach school.
Dixon suffered serious head wounds and has blurred vision, his mother, Thomasina Dixon, said outside court. He has had surgery and may lose sight in his left eye, she said.
"He's not the same. He was in severe pain," she said. "The beating definitely should not have taken place. It could have been handled a lot differently."
An attorney for Higgins, Jamie Rosner of Patchogue, said the fight was instigated a week earlier when he said Dixon harassed Higgins' sister, 14, a student at the school.
"This is nothing more than a fight between kids," Rosner said in court. "It had nothing to do with the fact that the alleged victim was gay."
The Dixon family has filed a $10-million notice of claim against the William Floyd School District, alleging security officers failed to keep Dixon's assailants out of the school.