Easy, Rossi is a faster Motorcycle Racer than Stoner.
To answer your question correctly we would have to put them on all types of Motorcycles and see. Which as they are only competing in one series, one very regulated series, it is impossible to determine completely.
Stoner has regularly been the fastest in one era, and has 1 800cc title, but not the most successful, nor does he have a 250cc title or a 125cc title. He also as yet does not have a title on another manufacture's bike.
At present the question should be more along the lines of, Is Jorge a better racer than Rossi? Jorge has 2 250cc titles and 1 800cc title on different manufactures.
Rossi has Titles in all classes across several Eras, including the deadly 500's. He is by far a better Motorcycle racer than any of them. And by racer, I mean Speed, Psychology, craft and consistency. There is no other current rider who has entered turn 1 in a race outside the top ten and gone on to win the race, Rossi has done this several times across all eras, Including last year at Malaysia-a feat which most thought never possible again on an 800.
Rossi has the unique ability to assess how fast he needs to go to win races and championships, he doesn't care who is fastest in practice, or even qualifying. Of the current crop of competition the only other Rider I feel who posses this ability is Jorge.
Not only this, Rossi could have retired several times to another Motorsport or to sit on his boat with his millions, with his record as GOAT of the modern age in tact. Yet he continues to compete with far younger and very talented challengers, and as is now-chase them down, injured, bulimic and another year older on a very quirky Machine in a heavily regulated series full of extraordinarily complex technology aiding riders performance..... This is something which is rare indeed, in fact of the modern greats, None have tried it and been successful on four manufactures, or even two......Rossi has less to prove than most riders in History, yet he is still out their trying....
Rossi's move to Ducati shows the true competitive spirit of the man and his team who follow, Most of his fans including myself thought he was mad, most of us still do! But it also takes a lot of 'Crazy' to succeed in this game......