What do you mean by "winners...over the years"? All of history? And I assume you mean completely clean their entire career. Not like David Millar who obviously doped, and I believe is clean today. I also presume you also aren't looking for some of the younger riders on a team like Team Type 1, who I believe are completely whistle clean.
If you only mean "Tour" winners, I'll say Lemond is a very good place to start. I'm convinced Greg was completely clean, and rode in an era of minimal doping, and most doping done at the time was much less effective than blood boosters since about 1991 actually - the year he was as fit as ever, and could barely keep up in the Tour, and in 1992 couldn't even finish.
Staying back during that era, and looking beyond Tour winners, I'm going to guess Andy Hampsten never doped, probably true with all the 7-11 riders.
Christophe Bassons was on Festina and refused to dope. He even refused to play ignorant, look the other way, and allow them to dope him without informing him what it was.
Giles Delion was very health conscious and refused to dope in the 1990s as well. Willy Voet apologized to him and said if everyone were clean, Delion would have won the Tour. He won the Maillot Blanc in 1991. His career ended about three years later when he couldn't keep up with the peloton anymore and he was forced to retire, at the age of 27.
I'm going to guess that after Tom Simpson's awful death there were a lot of clean riders in the late 1960's. Not all, but small dabbling in uppers until cortisone shots got popular. In the 80's we probably saw some of that, and some off-season light steroid use.
Before that, riders in the 40's and 50's, who knows?
The olden riders were all half drunk, and on God knows what, but still tough as nails.