You raise some good points, jhuskey--there is definitely much more rider support on and off the course during the race in modern times. However, I think that there is also much better training prior to the race--much more advanced techniques, science and diets go into the training to produce riders that, IMHO, are much more capable than riders of the past. That's not to denigrate riders from years ago, nor their accomplishments.
That said, to answer the original question, I think hands down the best TdF rider is Armstrong. Until someone puts 8 on the board, he's the man on top. No question that he avoided the other big tours to save himself for the TdF, which, in my book, probably drops him several places down the list for overall best riders. I also think the question of whether or not he doped is a dead question--too many negative tests, and too much time has passed for testimonies to be accurate or believable.