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.