We've been to both, and in fact will be doing both again this November --
but if you need to pick one -- shhhh -- pick Sharks! The room is more open, the tank is bigger, it IS cool to see all those sharks, and the food is wonderful. We often feel that SeaWorld was able to see what they did at WDW and then learn lessons and improve upon things. Not to say that we don't love WDW because we do, and we always stay on-site, etc. But somehow Sharks took the good idea from Coral Reef and managed to pull it off just a BIT better.
Are you already hip to the reservation system at SeaWorld? You make your reservation day-of, at the park, so take care of that first thing. Have a great time!