Hi,
If you are currently using glass aquariums, I would recommend getting a 300 gallon stock tank or something of that sort. If you could build a pen and use hard plastic pool liners, that would work too. Where do you keep them? Are you able to "make a mess". If they are in the basement or something, then you can build a pen and use pine/cypress mulch as a good substrate and use a hard plastic pool liner to hold water. Make sure that wherever you put them you can keep the area properly heated. Then once you have done that, then you can use some plants and whatnot. The alligators won't be that small for long so, look forward to them rearranging the "furniture". As far as heating elements, they have 250watt infra-red heat emitters, incandescent or blacklight bulbs, etc.
Fluval makes really good filtration systems. I would recommend 500gallon or more per hour filters at minimum.
I donot recommend glass water heaters. THEY BREAK ENTIRELY TOO EASY. Jack's aquarium and pets sells titanium water heaters with a connected rheostat. These I would recommend over most of the others I have seen. In any case, make sure that the crocs don't have access to the heater itself.
If you use rocks, make sure that they aren't too big. Crocodilians will ingest stones on occasion. It helps with their digestion. You don't want anything that they can end up getting injured on.
In anycase, I would recommend trying to keep things simple. The more you put into it the more they have to destroy, and believe me, THEY WILL WHEN THEY GET BIG ENOUGH! 3 foot gators are not big enough to do much damage right now. But they will be soon enough.
Good Luck and have fun.
Chris