For 2000s, do you really mean red Bull? After all, they only won their first championship in 2010- but utterly dominant from 2010-2013.I will limit myself to the decades that I actually observed:
1960s: Clark. The best driver I have ever seen competing against the most talent-laden fields.
1970s: The toughest call. It could be Stewart, Lauda or Andretti. I will go with Andretti because, in several of the Chapman biographies I have read, he credits Andretti's engineering talents and feedback with bringing Lotus back from the dead following the debacle of the Lotus 76. And I was a HUGE Lotus fan.
1980s: Prost. There were numerous accounts in various motor racing magazines of the period which said that, when he and Senna were teammates, Senna frequently (before their falling out) went to Prost to find out how to set up his car. Plus, Prost made it all look effortless, while Senna drove more with his balls than with his brains.
2000s: Red Bull
2010s: Mercedes: Since the turn of the century, IMO, the car has been the primary determinant of the Championship. The fields have been getting weaker with the overwhelming presence of pay drivers, and the proliferation of driver aids (those buttons and knobs on the steering wheels aren't ther for looks) have made the driver an ever smaller part of the equation.
Ferrari on the other hand from 2000-2004...