The comparisons are hypocritical because both built their careers on doping.
And arguing who was better is one of the fun things about the history of sports. I do it myself when comparing fighters of different eras. Joe Gans vs Roberto Duran or Duran vs Mayweather Jr. Fun alright but at the end of the day it's speculation at the top levels of any sport.
So if you're going to compare the accomplishments of Armstrong & Pantani you're going to have to do it in the context of two drug cheaters during the EPO era because those are the undeniable facts.