I'd say they were both very good.
Stuart was clearly more charismatic and comfortable with attention, well-liked, etc. Stuart showed strong abilities in intelligence functions. Stuart organized and built the cavalry of the ANV. In an emergency, he took over Jackson's Corps in the middle of Chancellorsville. He was, effectively, Lee's intelligence chief. He was also an excellent cavalry commander in the field.
Hampton became an excellent cavalry commander during the war (Stuart had the advantage of a West Point background and several years as a cavalry officer before the war (Mounted Rifles, then the 1st Cavalry). Always a determined fighter, Hampton's troops seemed more disciplined in combat. After the death of Stuart, the ANV cavalry might have become a bit more determined and hard-nosed in combat, particularly dismounted combat -- but they had been pretty good under Stuart as well. Maybe it was just the changing nature of the war in 1864.
In any case, if you are looking for a man to be the head of a cavalry force for the ANV, Hampton and Stuart would both be excellent choices, probably the two best the Confederates had for that position. If there was a third, it would be Forrest. There was somebody out west who was pretty good, but I don't see the background to judge him on for the ANV position. Wheeler, plain and simple, was not as good as Stuart, Hampton and Forrest.
All IMHO, of course.