I think your likely to need the whole day there.
The shows will all be popular but with a baby as well I would advise getting to them EARLY and making sure you get seats in the shade and take on fluids as it will be unbearably hot otherwise. Try to plan the indoor exhibits for the hottest parts of the day these are Manatees, Peguins, Sharks and Wild Arctic ( there is a seperate line for Wild Arctic as your kids will probably be too small for the simulator ride first) . I think your 3Y old will love the tide pool ( it's a small hands on exhibit where the kids get the chance to handle some sealife) and feeding the dolphins is going to be A BIG THRILL.