Look at Scooter's uncle, J.P. Gross (a clearly human muppet), I would assume they would both be the same species.
Scooter (and skeeter for that matter) are strange looking characters. But then again so are many other "human" muppets. Scooter is orange-ish (but some human muppets are green, pink, blue, yellow, ect.). He does not have a real nose and his head, ears, and hair make him look a little more animal-like than human (his face shape kinda reminds me a fraggle more than a human). But he is a human muppet. It is one of those things that is better not to think too much about and just kinda go with it.