Alfonso Lainer, 23, was arrested Tuesday and charged with aggravated harassment and assault as a hate crime, police said.
Elliot Morales, 33, pleaded not guilty to murder as a hate crime in the fatal shooting of 32-year-old Mark Carson.
Gay pride was on full display at the 21st annual Queens Pride Parade.
Gornell Roman was charged Wednesday with assault and aggravated harassment, both as hate crimes, police said.
The incident happened around 5:20 a.m. Tuesday. Police said a gay couple, ages 41 and 42, were walking on Broadway near Prince Street when two men began yelling anti-gay slurs.
A community is rallying against hate, and police are increasing patrols in some neighborhoods – in the wake of five anti-gay attacks in the past two weeks.