Lemond was almost certainly on the same uppers that all the other 80s cyclists were on. "A dog in a hat" spends a portion of the book talking about the drug culture in the late 80s, and to some extent, implicates lots of the guys who were successful in the 1970s.
I think there is probably going to be a spectrum of "clean", and it would be very rare if a winner of the TdF wasn't pushing the boundaries of what was permissible. My guess is that the last time there was a truly "clean" winner of the TdF, was whenever PEDs were so unrefined that they didn't really provide much of an advantage... so... maybe the 50s or 60s?