On a per-minute basis, definitely. The big difference is that LMA is out there on the court 8 more minutes per game. If you put Duncan on the Blazers, that means we'd be seeing 8 more minutes a night of Leonard, Hickson and Babbitt, and that's a drastic dropoff in talent. We'd get absolutely killed, even with the added per-minute productivity of a PF playing with a 24 PER.
Then you add in that Duncan has missed 9 more games this year than LMA, and it's even closer. Imagine starting Hickson and Leonard all those nights with Babbitt and Freeland backing them up. Ugh. That's 9 losses right there.
I can see an argument for either. On a team with a lot of talent like the Spurs, Duncan is superior. On a thin team like ours, Aldridge is the better option. I don't think there's a clear-cut "Best PF" overall because they both fill such drastically different roles.