There Will Be Blood, and it's not even close. I love Boogie Nights, I love PTA, and I may even prefer The Master to TWBB in the end, but if it's between TWBB and Boogie Nights, there's no contest for me.
One thing that wasn't mentioned during the episode is just how funny There Will Be Blood actually is. It's not an airless, austere work with pretensions towards being a masterpiece - it's a deeply funny, humane, quietly tragic film that remains utterly singular in the world of film, and is well-deserving of a place in The Canon.