There are alligators all over WDW -- usually not big huge 6-footers, but there are some of those as well -- anywhere in Florida there is open water, you'll find alligators -- they live in the water but can walk on land wherever they want -- no way to keep them out.
I've seen them in the back waterway to the left of the train in MK; there is a big one that lives in the big pond in front of Riverside, sometimes you can see it from the bus.
I've also seen them at Animal Kingdom in the waterway near the old boat landings.