Well, I'm not actually totally sure.
First of all, where does CC Sabathia rank? Do you discount him entirely because he changed leagues? Count him for the NL because that's where he (was best / finished the year)? Count him for the AL because that's where he threw the most pitches?
Cliff Lee would seem to be the clear cut favorite even by our lovable new metrics. After all, he's the only AL SP with a tRA under 3 and his pRAA blow away anyone except for Sabathia's combined total. But there's an important factor first brought up by Royals Review and echoed by Geoff Baker recently, that is the strength of competition. Royals Review went ahead and grabbed the actual numbers for us, so I'll just quote him:
Lee's average challenger was a .262/.330/.405 hitter.
Halladay's average hitter was a .266/.342/.425 guy.
Well, how big of a different is that actually? It doesn't seem like much, but remember this is the average difference, manifested over nearly 900 batters faced. Small margins add up over a sample that big. I wanted to put an actual number on that and since I only had triple slash lines, I went to GPA since I knew that could handle those inputs and give me a decently good figure for the difference in runs. (See THT Glossary for formula).
Taking the difference in runs per plate appearance for those two hitters, I multiplied that out by the 987 batters that Halladay faced and ended up with a difference of about nine runs. That is, if Roy Halladay had faced the same average hitter that Cliff Lee had faced, you would expect Roy Halladay to surrender nine fewer runs.
Nine runs chopped off Roy Halladay's line lowers his tRA to 3.04, which is still slightly higher than Lee's, but Halladay faced more batters. It also likely vaults him ahead of CC Sabathia (I don't have CC's average hitter line, but given that half his season was in the NL and the other half was spent facing the same batters as Lee, I would be surprised if it was anywhere near high enough).
Basically you have:
CC Sabathia at about 46 pRAA, but half accumulated in the NL
Cliff Lee with 43 pRAA and the lowest tRA
Roy Halladay with 44 pRAA and the most batters faced