El Duque was pitching with a bad shoulder, and gave up three runs in the fifth inning before exiting in Game 4. Mussina was decent in Game 5, but gave up two runs in the first inning, and couldn't complete seven.
Sure, Jon Lieber and Mike Mussina pitched well in the series, but they were average pitchers that season. Here are the ERA+'s of each teams top three starters that year.
Yankees:
98
104
110
*Two of those guys missed time in September, and the one with the best ERA+ is Kevin Brown...
Red Sox:
150
125
121
Regardless of what happened in that series, the Red Sox's starting pitching was clearly superior to what the Yankees had.
Again, I'll reiterate my position once again. The greatest comeback in MLB postseason history is the 2004 Red Sox in the ALCS. In all likelihood, nothing will ever match it. All I'm saying is that the Red Sox, on the strength of their starting pitching, were the better team.