You need to place the camera lens up against the glass to avoid reflections. You accomplish that by using a lens hood, preferrably rubber to give a good seal and allow you to angle the camera. The widest angle lens you can use would be the best because of the refraction of the water will make it seem longer than it is, or the fish larger than they are.

Additionally you can use a dark tee shirt or towel to block reflections if you have to stand back.

Without being able to hold the lens against the glass, the best you can do is shoot high ISO and hand hold, shooting available light. Flash won't work at all.

It's been a while since I've been to Sea World, but I believe that you stand on a moving sidewalk to go through "Shark Encounter". That makes it difficult to set yourself up in a good position for shooting, although you should be able to go through as many times as you like.

Shoot high ISO and hope for the best. A circular polarizing filter would cut down on reflections, but it'll also further darken an already dim scene. One other thing - shoot STRAIGHT. Those acrylic panels which make up the tube may be pretty clear, but they're also about 12" thick and will wildly distort if you shoot at an angle.

But don't despair. There are LOTS of places in Sea World where you can get right up against the glass and take great shots of lots of colorful sea creatures. The Shark Encounter simply doesn't happen to be one of them.

And let me plug a local attraction if I may. The Florida Aquarium in Tampa is well set up both for kids and for photography - particularly the Coral Reef exhibit which puts you at the bottom of the reef looking in - and you can swim in that reef for only $75... It's not Sea World, but it's VERY well set up for kids. About an hour and a half from Orlando by car.