I think it depends on what you mean by best: Talent? Guts? development ability? race statistics? It's very hard to compare riders from different eras, as they face(d) different challenges.
Also I agree that Rossi is racing in a period where there is less competition, it may be rose tinted spectacles but Lawson, Gardner, Rainey, Schwantz Doohan etc seems stronger competition than the current lineup.
I have heard that some of the Honda bosses thought Freddie Spencer was the best of all of them, if it wasn't for injury he might have gone on and on. Equally Doohan could have actually had his leg amputated and never won anything in GP.
My personal favourite is Doohan, just because of what he's gone through to get to be GP 500 champion. If he hadn't had the massive injuries, I think he would have dominated even more.
But you could say something similar about Rainey....
Agostini?
Mat.