Muhammad Ali may have been the greatest pure athlete ever to earn his living at boxing; that is not the same thing as being the greatest prizefighter or even the greatest heavyweight prizefighter of all time. He never had any sort of a punch with his left hand which could really hurt anybody and he never had the combinations of heavy punches which you see guys like Roy Jones, Duran, or Gennady Golovkin using.
I personally view Duran as the greatest prize fighter of all time and, until somebody holds the heavyweight crown for 13 years, I will view Joe Louis as the best heavyweight.