That's a really, really tough question. On the one hand, prime Tyson is easily the most dangerous fighter ever...on the other hand, prime Ali was the greatest ever at doing the kind of things he'd have to do to defeat Tyson.
Ali was the most evasive heavyweight ever- he could dodge most attacks and fall back quickly to reduce the power of an opponent's punch. Ali also had the greatest chin in history- he stood up to poundings from Foreman, Shavers, etc. Tyson's one-punch power might not have brought Ali down.
Ali was also the best at head games. Tyson was frightening but easily frustrated when intimidation failed. Tyson's laser focus might have failed if Ali proved a tough nut to crack.
Ali was a master of endurance and pacing, while Tyson was known to burn out. Knowing this, Ali would dance for ten rounds to exhaust, confuse, and enrage Tyson. Once Tyson was mentally disconnected, Ali could jump in for a quick kill, just like he did with Foreman.
And, of course, Ali had a massive reach advantage on Tyson, which would play right into Ali's game plan.
To get some idea of how Ali would have fought Tyson, watch the first Holyfield fight. Tyson was never really in it, and nobody is going to say that Holyfield was as great as Ali. Of course, that was post-Cus, post-Douglas, and post-prison...Tyson was perhaps even more dangerous than he used to be physically but past his prime mentally.
I think that, at the very peak of his powers, Tyson had about 2-1 odds to defeat Ali, but no shot at all post-Douglas.