"there was cheating right from the start" (l. armstrong in his autobiography about the history of the tour) Some times ago I believed that this is a hint ...
My really rough estimate based solely on google searches for riders and doping comes up with this as a list for potentially clean highest placings...
1999 Daniel Nardello, 7th
2000 Daniel Nardello 10th
2001 Andrey Kivilev 4th (Died 2 years later in a crash in Paris-Nice).
2002 David Moncoutie 13th
2003 Peter Luttenberger 13th
2004 Sandy Casar 16th
2005 Cadel Evans 8th
Not claiming this is 100% ac curate. But it does suggest Armstrong's comments about everyone doping could be taken to hold for almost everyone in the top ten places in each of his years.