He isn't based of an "animal", he is based of a human. For a start, he looks like your average tenager, board, has a hoody, looks kinda like a punk. He is also known as the hoodlum Pokemon. Hoodlum means a criminal or a gangster, and I have never seen, nor heard of, a gangster/criminal animal, as only humans have the mind to do this.
However, he also seems reptilian, having baggy, scaly skin. He doesn't have any nose, rather two holes (like a lizard) on the front of his face. He also has a tail, a thing all reptiles have, and can only be found as a mutation in humans. He has a bright crest on top of his head, like the frilled lizard, in the shape of a mohawk, and seems to be a sign of dominance. Although these frilled lizards do not use it to determine the leader, they do use them to hopefully gain dominance over it's attacker. And guess what? It gets intimidate, like the frilled lizard. It also gets Moxie (gangster?) and Shed Skin (LIZARD).
Lastly, some predatory lizards could be described as, well, gangsters. Even Bulbapidia descripes him as lizard like.
Scrafty is a bipedal lizard-like Pokémon. It has oval, wide-set eyes with small pupils and gray eyelids, as well as small nostrils and a wide mouth with bared teeth. It sports a red crest on its head, similar in appearance to a mohawk. Baggy yellow skin hangs off its shoulders, falling halfway down its back. Scrafty's body is orange, with thin arms and a gray, scaled belly. Its lower body and tail are covered by loose yellow skin resembling baggy trousers. On its tail is a single red scale.
From this, we can see he is a bipedal, human-like lizard. He must have some sort of brain, as he seems to know he is a gangster/criminal and chooses to act like it, making him rather intelligent compered to other animals. In fact, he seems like a lizard with a human brain, and is able to think/act like a teenage person, laking only facial features, lack-of-tail and speech.
Sorry if I got a bit carried away ;)