Overall I'd have to say George Carlin was the best, because while his stuff was raunchy at times, there actually were bits and pieces of social commentary in every bit he did. Even his most famous bit ("7 Dirty Words You Can't Say on TV") was born out of a want to highlight hypocrisy in social norms.
So he was really the "thinking man's comedian", and my favorite by far. After that I'd have to say Daniel Tosh, Dave Chappelle, Eddie Murphy and Nick Swardson round out my top-5