Both are good on attack (I've powered one of each up and use them all the time).
Powered up to 2500ish they're not as squishy.
If you prefer Vaperon with Hydo you'll probably prefer Thunder. If you prefer Aqua Tail...
I tend to base which I use on the defender (if I know it) - i.e. if they use single bar I'll go Thunder, if they've got multiple bar attacks I'll take advantage of dodging and go 2 bar too.