Ironically enough, we visited both on our last trip (11/02). Probably the biggest consideration for you might be distance from your hotel. Gatorland is much closer to WDW than Jungle Adventures.
Would you be going specifically for the alligators? If so, then Gatorland would probably be fine for you (they also have a pretty neat walk through a swamp).
If you want to see more animals then Jungle Adventure might be a better bet. They have bears, panthers, raccoons, etc.
If you have other specific questions, I'll be glad to help.