William Robbins and Dyson Williams are being held without bail after pleading not guilty Wednesday to murder, robbery and other charges.
Prosecutors say both men are responsible for Sister Mary Celine Graham's June 22 death, because both allegedly were fleeing after a string of stickups.
Robbins got out of the car when police pulled it over.
Authorities say Williams then got behind the wheel and sped off, causing a crash that killed Graham as she walked on a Harlem street.
Defense lawyers say Williams denies driving, and Robbins shouldn't be considered a conspirator.