In terms of tragic outcome for the character, there are two ways of looking at it, I think. You might judge between the two in terms of which character is more sympathetic to the audience/reader. You might also judge based upon who behaves in the most dastardly way so as to deserve his tragic end. It's not possible to judge based on their ends because they both pretty much end the same way: eternal damnation and everlasting infamy. Macbeth may start out as the more sympathetic character, though he may fast fall from favor starting when we see how he is manipulated by the base arguments of a blood-thirsty Lady Macbeth. Dr. Faustus may seem a less sympathetic character at first because he is "only" a scholar, yet, though he makes a deal with Mephistopheles, his actions that consume him are seemingly not as horrific as Macbeth's. One possible conclusion is that since Fautus' flaw was primarily in judgement while Macbeth's was in judgement that was followed up by manslaughter, Fautus might be more tragic as being less deserving of his end.
Macbeth is the greater play, I think. It's much more widely staged, taught, and reviewed by critics. It generates hundreds of pages of criticism not only in literature and drama, but also in history, psychology, philosophy, and the social sciences.
Macbeth is much more modern and humanistic. Faustus seems stuck in the mythical, supernatural, and Medieval.
For whatever it's worth, in Daniel S. Burt's The Drama 100 : a Ranking of the Greatest Plays of All-time, Macbeth was ranked #5, and Doctor Faustus was unranked. That shows you the disparity.
I think Faustus is a greater play because it not only shows the fall of the eccentric scholar Dr Faustus but also anticipates the fall of modern man who is the off shoot of renaissance man.
But I need a few clear reasons behind a support. if you go for any, why do you support that?