Authorities said Raymond Kenner, 22, had blood on his clothing and a folding knife in his pocket when he was arrested in connection with the killings.
Queens District Attorney Melinda Katz said in a news release that video surveillance implicated Kenner in the Dec. 21 killing of 25-year-old Andrew Cunje, in Hollis, and the fatal stabbing just two days later of 29-year-old Benjamin Vasquez, in Jamaica.
Prosecutors also charged a second man, Alexander Stephens, 31, in Cunje's death. He was wearing bloodstained boots when he was arrested, Katz said.
Both men pleaded not guilty Thursday to charges including second-degree murder, robbery and tampering with physical evidence. Messages were left with their defense attorneys seeking comment.