From Animal Planet:

Q: On Alligators vs. Crocodiles

My name is Michael. I am 8 years old. What is the difference between crocodiles, alligators and crocodilians, beside where they live and the shape of their heads?Thank you in advance for answering my question.

A: Michael, all species of crocodiles, alligators, caimans and gharials are known collectively as "crocodilians" (or more correctly "crocodylians") because they share many basic features. However, scientists have placed crocodiles and alligators in different families (crocodile in Crocodylidae, and alligators in Alligatoridae) based on key differences between all alligators and all crocodiles. Caimans incidentally are also a type of alligator, and gharials are in a family of their own called Gavialidae.

What are these key differences? They are mainly based around features of the skeleton and body, and you've already mentioned one of these — the difference in the shape of their heads. Alligators and caimans have broad U-shaped snouts, whereas crocodiles have narrower V-shaped snouts. There is some variation (for example Mugger crocodiles have a very broad snout like an alligator, and some subspecies of caimans have an almost V-shaped snout). Alligators are recognizable because the upper jaw overlaps the lower jaw, and hence all the teeth of the lower jaw are hidden from view and fit into depressions in the upper jaw. With crocodiles the teeth interlock more evenly, and those in both the upper and lower jaws are clearly visible when the mouth is shut. The large fourth upper tooth in particular is easy to spot in a crocodile, but not an alligator.

Did you know that crocodiles have salt glands on their tongue? They're actually modified salivary glands, and their purpose is to secrete excess salt from the crocodiles' bodies. Alligators and caimans have the basic structures in their tongues as well, but they are nonfunctional. This means crocodiles are — as a rule — more tolerant of saline water than alligators and caimans. At one extreme, saltwater crocodiles can spend many days or weeks in salt water if necessary. Alligators and caimans are almost totally restricted to fresh water. I don't recommend you get close enough to a crocodile's or alligator's tongue to find out whether it has salt glands!
Another difference lies on their scales. Both crocodiles and alligators have sensory organs called ISOs (integumentary sense organs) covering their head and particularly their jaws. Look carefully at them and you'll notice a myriad of black spots, almost as though they need a good shave. These are the ISOs. They enable the crocodile or alligator to orient the head toward pressure changes in the water (e.g. a water splash at the surface). Interestingly, crocodiles have similar organs covering their entire body (one on nearly every scale of the belly, the flanks, the legs and even the tail), whereas they are absent from the body scales in alligators and caimans. If you look at crocodile leather, you can clearly see a small dimple on every scale, but not on alligator leather.

There are many differences between crocodiles and alligators, but these are probably the most important ones that affect not only our ability to tell them apart, but also their ecology and behavior.

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