What eye color should I put on my license if I have different colors each eye?

Not critical. Eye color is one of those identifiers that cannot be changed so it is part of the license listing of the individual. Is one of your eyes a different color because of a nevus (it will be brown), or due to injury or internal iris disease, or is there truly a difference (rare but possible for instance in a sympathetic nerve disruption due to forceps delivery). Use your best guess of base color.
Ask DMV agent. Ask the dmv agent. There may be special provisions for that in your state.