Was just discussing this with a friend, and actually realized there's a pretty viable argument for both players. Of corse, I'm referring to Santana in his prime, when he won the Cy Young in '04 and '06.
I know there's a lot of stat people on here, so just wanted to get your take.
Stats comparing Cy Young seasons-
Lincecum- '08: 2.48 ERA, 265 K (10.51 K/9), 84 BB / '09: 2.48 ERA, 261 K (10.42 K/9), 68 BB
Santana- '04: 2.61 ERA, 265 K (10.46 K/9), 54 BB / '06: 2.77 ERA, 238 K (9.44 K/9), 47 BB
You guys probably have more advanced stats you look at, just felt like giving a baseline. It's not much to base on yet, but here's the graph for ERA by age comparing Lincecum or Santana
(sorry if it's hard to read, but you get the point- made it bigger, less clear)