Depends on how you look at it. Lee was very good last season coming off a ridiculous 2008, but he had the benefit of pitching against some VERY mediocre offenses in the AL Central and then moving to the National League. Beckett has to do his work in the ALE year in and year out.
Beckett's 2007 was on par with Lee's 2008, IMO, he just didn't have the gaudy win totals to match Lee. Lee will continue to benefit from facing mediocre offenses and will now pitch in an insanely friendly pitching environment (when you factor pitching & defense). Hell, this is the team and ballpark that made Jarrod Washburn look like a passable starter last season. No small feat.
I think people in this thread are really undervaluing Beckett. For about three months last season, he was one of the top two or three pitchers in all of baseball. He got hurt, and got derailed a bit before recovering in September. He had a good playoff start against the Angels. Obviously not on Lee's level, but Beckett definitely wasn't some scrub last season.
I'll bet dollars to donuts that Beckett is better than Lee in all of the fielding independent pitching statistics this season.