Read the Tyler Hamilton book ("The Secret Race"). That's the book which really brought down Armstrong.
In it he makes clear how much better organized the US Postal Service team was than anyone else (except maybe T-Mobile and ONCE).
When he left and went to Phonak he was on his own and had to organize his own doping (which went pretty badly).
Yes it's true that there were no clean winners in that era, but there were clean riders. Christophe Bassons' book talks about it a lot, but Wikipedia has a decent summary[1].
It's also worth noting that there are no real allegations of drug use against Pereiro, Sastre, Andy Schleck, Evans and Nibali, who all rode against Armstrong or immediately after him.
[1] https://en.wikipedia.org/wiki/Christophe_Bassons#1999_Tour