Whatever you do, stay away from the aquarium in Key West! You pay $9 per person, and all it's just one big room! You literally walk in the door, stand in the middle of the room, spin in a circle, and you've seen the whole place! Of course Key West also has the coolest "aquarium" I've ever been to--diving on Looe Key
The Baltimore Aquarium is the best I've been to, but I haven't been to many different ones to judge. I'm going to volunteer there as soon as my wife gets a full time job (she's student teaching). They take certified diver volunteers to feed the sharks and rays! I'll probably just be helping maintain the tanks though.