The three face up to life in prison for a variety of federal charges, including the use of explosives, arson and civil disorder.
Samantha Shader, 27, is accused of throwing an explosive at an NYPD vehicle while four officers were inside it in the early hours of Saturday, 30 May.
Urooj Rahman, 31, and Colinford Mattis, 32, both lawyers from Brooklyn, are both accused of throwing Molotov cocktails at an unoccupied police vehicle on the same night.
“Such criminal acts should never be confused with legitimate protest,” said US Attorney Richard Donoghue in a statement. “Those who carry out attacks on NYPD Officers or vehicles are not protesters, they are criminals, and they will be treated as such.”
New York witnessed violent protests across the city following the killing of George Floyd by a Minneapolis police officer on May 25. That initial burst of anger was followed by larger and more peaceful demonstrations that continue to this day.
Although no one was injured in either of the incidents, the FBI said Ms Shader allegedly threw a Molotov cocktail which shattered two windows of an NYPD vehicle while officers were inside.
Prosecutors said Ms Shader "has travelled the country committing various crimes, which include acts of violence and resisting arrest.”
The FBI said Rahman and Mattis threw their device into an already damaged NYPD vehicle, setting it on fire, before fleeing in their van. They were apprehended the same night, according to the charge sheet.
New York has seen a historic spike in arrests since protests calling for racial justice began — nearly half of which were for breaking a curfew imposed in the city to restore order. According to the Gothamist, 1,349 New Yorkers were detained for violating the curfew. Across the country, more than 10,000 people were arrested up until 4 June.