IMO, to close to call as both have strengths and weaknesses when compared against the other, plus we are talking different eras of tyre and technological development.
For mine, Stoner was what Marquez is today, blindingly quick, exceptionally skilled and a man intent on pushing the limits to their maximum.
Stoner was extraordinary in his bike control and as many learnt later is his career he was a user of the absolute minimum electronics (traction control etc) which means that his throttle control and feel for the bike are amongst the rarest of the rare. Suppo and others have told stories of Stoner's innate ability to know what to do and when in terms of practice, plus the feel that something was not right with the bike. He was a freak in so many ways, and that is before we talk of the style on the bike
Marquez is for me the modern Stoner in terms of his raw speed but he is unlike Stoner in that he uses higher lean angles and at times seems more 'out of control' (no criticism) but is obviously very in control. He is able to do things on a bike that make your jaw hit the ground, he has the bike more out of shape than a chocolate bar in summer, he is a spectators' delight in so many ways.
To me, the decisive factor would be tyres and era in which you compare as like all things, these move on and therefore make comparison impossible to decide who would beat who.