I happen to prefer "indices" but I was wondering if one was generally preferred over the other.
Who are you writing for? That should be the first consideration. For example, opening the Oxford Writers' Dictionary, I find that it tells me to use the plural "indexes". So if you're writing for Oxford University Press you'd better use "indexes". If you're writing only to please yourself you can use whatever plural you like, so in theory you could be like those people who write "unixen" and say "indexen" I suppose, although that might make your writing less popular.
I think "indices" is common enough that it doesn't come across as at all an eccentric choice.