The rock cracked a window on the side of the bus. The students attend Bais Rivka, a Chabad school.
A second bus driver witnessed the attack on Tuesday and described the teenagers to police, COL Live reported. The driver of the bus that came under attack filed a police report.
Police are seeking the teens on criminal mischief charges, WABC-TV reported.
Brooklyn, notably in Crown Heights, has seen a rash of attacks against identifiable Jews in recent months.