Comparing two players straight up without the need of including "what's best for the Red Sox" is not strange or rare in this place, a baseball discussion forum.
The straight up question of : "Is Lee better than Beckett?" is a simple one to answer using statistics, and the fact that Beckett plays for the Sox does not give him a 20% boost in statistics. I'll say it again, in a player-to-player comparison, regardless of team issues, who is the better pitcher? That is easy to answer without trying to cop-out from the discussion E1. The "potential signing" line is not part of the discussion, just a straight up comparison:
Cliff Lee, 2007-2010:
109 GS, 764.2 IP, 3.40 ERA, 125 ERA+, 1.17 WHIP, 7.1 K/9, 1.5 BB/9, 4.60 SO/BB.
Josh Beckett 2007-2010: 110 GS, 715 IP, 4.08 ERA, 114 ERA+, 1.23 WHIP, 8.6 K/9, 2.2 BB/9, 3.91 SO/BB.
So in the discussion of "who's the better pitcher" it's clear that Lee is the better pitcher. It's really that simple.
You can make the argument that when healthy, Beckett has the potential to pitch to a level similar to Lee for a fraction of the cost, you can make the argument that he's younger, so he has more prime years ahead of him, but regardless of salary or age, Cliff Lee is currently the better pitcher, and there's really no way to argue that.