I vote "indexes"
Since it's a toss-up, I plan to use "indexes" from now on.
Chris Ballance argues in a comment above that "indices" is easily distinguished from the verb, as in "he indexes things", but I think that would be clear from context.
Meanwhile, "indexes" is a normal-looking plural and "indices" is a weird exception to learn. Languages tend to drop the least-used oddities over time, and I think that's a good thing. Goodness knows we still have plenty of oddities to remember. Think of all the poor toddlers hearing "it's not 'eated', it's 'ate'", and embrace simplifications when you can.