I'm not in either field, but a belief in universal "deep structure" has helped me learn both language + music stuff. Even if they don't exist, I'm going to stick with what helps me :D
I can't really think of anything that universally defines "music", other than that it's sound with an aesthetically pleasing structure.
I don't know about Chomsky, but I took a linguistics course and the universal grammar was a major part of the course. It seems you're implying there's no such thing, what makes you think so? The impression I got from the course is that the idea of "universal grammar" is universally accepted (among linguists, of course).
http://en.wikipedia.org/wiki/X-bar_theory
Ironically I don't remember Chomsky's name coming up during the course at all.
Although to be honest I probably ignored names on purpose because there were so many of them.
Have a look at http://www.youtube.com/watch?v=A13_QGMtlRE. I think Bobby McFerrin would say that there indeed are music universals.
Counter-example don't disprove trends, though, and there are certainly trends (I think "universals" is just not quite the right word).