If you pitted both men against each other, Mourinho comes out on top as he has a very good head-to-head record vs. SAF.
If I had to choose, I'd probably go with Ferguson. For him to achieve what he has, at one club, for 26 years and still be wanting more is something that won't be achieved again in the game. Like people have pointed, the culture he changed at the club but also evolving as a coach, embracing technology and science to better his squad, building 4/5 teams over the years, handling volatile characters and being ruthless enough to discard them when they got too much, and bringing through younger players into world stars such as Ronaldo, Giggs, Beckham, Scholes.
Mourinho is very difficult not to admire. His trophy haul is I think, half of what SAF's won in a shorter space of time but he could beat it if he carries on in this vein. He's had these pitstops over Europe (starting off in Portugal, England, Italy, Spain) and won trophies but the fact that he's not carried on at a club for whatever reason, to win more, build a new team, bring in players from the youth system etc means there is a doubt hanging over him whether he can deliver success over a prolonged period at the very top.
He's at Real Madrid now, probably the biggest club in the world and one that has a tremendous attention on it from the local media. If he leaves at the end of this season, he'll go to another club and probably move on again from there.
People talk about Varane, is that really a vindicating reason to say Mourinho favours youth? Varane only joined Madrid because Zidane talked and encouraged him to join not because Mourinho was so desperate to have him. Only at Porto, you could say Mourinho worked and developed Portuguese players but at Chelsea, Inter, Madrid - which youth players from those clubs has he integrated or worked with into the first team? I can't think of any.
He has said he wants to be at a club for a long period and if he does that, i.e stay for more than three years and accomplishes success whilst rebuilding teams, nurturing youth and experienced players and wins trophies at the highest level then I'd say Jose over Ferguson.
But that last paragraph, is one that remains to be seen.