Both players had careers that roughly coincided 1991-2009. During that time the difference in OPS between both leagues was about .020, especially considering the pitcher hits in the NL.
NL AL
0.689 0.724
0.684 0.713
0.726 0.745
0.747 0.779
0.739 0.771
0.738 0.795
.744 0.768
0.741 0.771
0.771 0.786
0.773 0.792
0.753 0.762
0.741 0.755
0.749 0.761
0.756 0.771
0.744 0.755
0.761 0.776
0.757 0.761
0.744 0.756
0.739 0.764
Sum 14.096 14.505
NL Average OPS 1991-2009 .742
AL Average OPS 1991-2009 .763
Another big difference maker is that Pedro pitched in the AL East between 1998-2004, and Mussina pitched there his entire career. The difference in OPS between the AL East and the rest of the AL was significant in its own right.
So, how do their careers fare differently?
My guess is that they pitch about 10 more innings or so a year, due to saved pitches against the NL batter and easier outs in the NL versus the AL East. The difference in ERA may be decent too. Andy Pettitte's ERA in the NL was 0.2 earned runs lower than the AL, and Roger Clemens was more than a half a run lower in the NL then what he was doing in the AL before and after. On the flip side of the coin, Randy Johnson's ERA ballooned when he returned to the AL by more than 1.5 earned runs, and then fell by 1.1 Earned Runs when he returned to the NL. Curt Schilling, bloody sock and all, saw his ERA increase by more than 0.5 Earned Runs going from the NL to the AL East.
So, in conclusion, Mussina's career ERA would probably be around 3.5 while Pedro Martinez might have been around 2.7.