Since I have been watching, B4nny, Clockwork, Stark and Mike and maybe even Kaidus standout.
But it's difficult because how do we quantify best? B4nny is top level on 3 classes, though you can debate whether he is best at any one (demo quite possibly). Clockwork and Mike are pretty much one class specialists (although CW could snipe brilliantly). Better than B4nny probably on those classes, but he can play three classes. Stark is imo at least comparable to CW on scout and not much worse than top soldiers on soldier. If he's on soldier he can contest Mike in a match, from what I have seen. And Kaidus was great and seemed to be capable of even more than he delivered at LAN, albeit rarely on the best team. Once again though, a specialist. I have omitted any medics, which seems unfair. I'd probably pick Shade, but I watched more NA TF2 than EU when I started watching a few years back.
So essentially, is a specialist better than a top level generalist? Not a clue.