The defendants are accused of attacking the brothers as they walked arm-in-arm to keep warm on Dec. 7.
They were arrested last week and pleaded not guilty to second-degree murder as a hate crime. They have been held without bail.
District Attorney Charles Hynes said it was not certain when they would be arraigned on the new charges.
The brothers were walking home from a bar after a party in the Bushwick section of Brooklyn. Romel Sucuzhanay had put his coat around his brother to keep him warm.
Phoenix and Scott, also leaving a party, pulled up in an SUV.
The two groups exchanged words and the fight escalated. Scott hit Romel Sucuzhanay with a beer bottle, and Phoenix savagely beat Jose Sucuzhanay with an aluminum baseball bat, prosecutors said. Jose Sucuzhanay died several days later.
Phoenix says he had acted in self defense because it appeared Jose Sucuzhanay was reaching for a gun. Hynes refuted those claims at a press conference attended by a slew of city leaders and activists.
Jose Arrufat, an attorney for the Sucuzhanay family, said they were thankful for the exhaustive investigative efforts.
The family is trying to pull together to care for Jose Sucuzhanay's children, 5-year-old Joanna, who has Down syndrome, and 10-year-old Brian.
"The family has suffered tremendously," Arrufat said in Spanish. "It was a brutal murder."
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