I'd have been fine with either. There is always going to be the case made that the best ability is availability and Pronger spent time in trouble and either in the box or suspended at times during that run. At the same time, as you said, the sheer dominance of his presence needs to be considered. I can't recall a player tilting the ice to that extent during a playoff run post-Lockout other than maybe Malkin in 09.
There have been more comprehensive and all-around better performances since, but from 05-07 Pronger changed the way the entire game was played on both ends of the ice.
Pahlsson was easy to forget about because the stuff he contributed flew under the radar. I think the entire checking line with Anaheim was incredible, but Pahlsson was taking on some offensive juggernauts during that run. I'd have been fine with him winning it, too.
Anyone but Niedermayer, honestly. The guy underwhelmed me and while he was admittedly a fantastic skater even then, at an older age, he wasn't even the best blueliner on that squad.