Both have their good uses, but if I'd have to pick one over the other, I'd go with Samurott, mainly because Megahorn. It's a decent Mixed set runner. Not terribly fond of the "horn" design on it's head, but otherwise I like the blades it has.
To me Carracosta has always felt too slow for my preferred uses. I dislike having to wait over the opponent. And sometimes it can be suprise-lethal if they pull out a grass move trick card that I wasn't expecting.