In my opinion Muhammad Ali was EASILY the better fighter. Don't forget the way he masterfully dispatched George Foreman in Zaire, I think it was, in the "Rumble in the Jungle." I don't know if Mike Tyson, a formidable puncher to be sure, who often had his opponents beaten (through intimidation) before the referee started the fight -- was really as good as we thought he was. I could be wrong, but that is my suspicion.
Also, you know the conventional wisdom (and we have no reason to disbelieve this to my knowledge) -- "A good boxer beats a good puncher." Even if we want to say that Tyson was a great puncher (which is still doubtful in my mind), Muhammad Ali was definitely a great boxer!