I think it will all come down to Lee's performance next year. If he regresses significantly, I'd avoid him, but if he posts another low 3 ERA, I'd prefer him. There's not much Beckett can do to influence my opinion. 2007 was a career year for him and he'd have to repeat that kind of performance to approach Lee the last two years.
2009
Beckett - 3.63 FIP, 5.3 WAR
Lee - 3.11 FIP, 6.6 WAR
2008
Beckett - 3.24 FIP, 5.0 WAR
Lee - 2.83 FIP, 7.2 WAR
2007
Beckett - 3.08 FIP, 6.5 WAR
Lee - 5.48 FIP, 0.2 WAR