IMO, as someone who was around the latter part of Ali's career & who's known Tyson since we were amateurs together back in the Empire State Games, I believe that Ali would stop Tyson in the later rounds had they both met at their peaks. Ali had the type of physical make-up, style, & mentality to do a number on Mike. I don't think that Mike could cope with Ali's movement, his jab, or his physicality. Ask any former Ali opponent about what surprised them most about him & they'll tell you his physical strength. And I think Ali would negate much of Tyson's offense by sticking him with his jab & then shutting him down every time he'd get close. Which would frustrate Mike & wear him down mentally & physically. Despite his smaller stature in height & his explosive handspeed, one of Tyson's biggest weaknesses was fighting on the inside. He didn't like to do it & he wasn't very good at it. Ali would eat him up at that range.
Of course, Tyson would be dangerous against just about any opponent in the early rounds by I just can't envision him ever being able to get Ali out of there in a round or two. So, it would go rounds with Ali controlling things more & more as it goes on until a frustrated, tired is battered into a defeat in about eleven rounds.