Pep's Barca was an incredible collection of world class talent perfectly suited to his playing style. That combination made those wins over United possible. I think it's ridiculous to use that as an argument for Pep being superior to SAF. Pep was unable to win the CL with Bayern and the jury is still out on Man City. Barca went on to win another CL title even with a slightly worse team and Enrique.
Of course, SAF's successes were also all with one club but he managed to keep ManU successful for decades. I don't want to go into an argument about who's the best coach of all time but Fergie is definitely a contender. Pep's among the best right now but only time will tell if he can repeat what he achieved in those three years.
I mean, of course ManU are going through a rough phase right now but that doesn't take away the fact that they were the standout English club for more than two decades. And I say that as someone who's lived in Manchester for some time and would always chose both City and Stockport County as my favourites over United.
Side note: I went to see the first division derby County vs. City in 2000, I think. Hard to believe given where those two clubs are at right now...