Darius Love and Anthony Williams, both 17, face battery charges from Saturday night's attack in the 600-block of East 71st Street.
Love also faces a felony robbery charge.
Police said the two and two 13-year-olds disabled the 71st Street bus by engaging a shutoff switch, got on the bus and began hitting the driver in the head with their fists.
No word what might have provoked the attack.
A witness on the bus helped police identify all four suspects.