Right now, I would say Ferguson by a small margin.
Ferguson is the dynasty master. No-one has done what he has done. Bob Paisley's record at Liverpool was arguably better, but was over a much shorter period of time - and sustainability is what football is all about. All around, managers aren't generally lasting very long - in the PL, there's Ferguson, Wenger and Moyes on more than 10 years. After that, there's Tony Pulis and then absurdly the fifth and sixth longest serving managers are Martinez and Mancini with 3 odd years.
No-one else seems to be able to sustain the level of victory with successive teams. Man Utd have the occasional off year (or two) but then they're back and winning things. Arsenal have been out of it for 8 years and are heading in the wrong direction, as are Chelsea. I'm not convinced by Man City's long term plans. The main thing about Ferguson's Man Utd is that they don't get bothered by defeat and they don't get complacent about victory. When they lose, they dust themselves off, get up and go again. When they win, they enjoy it and come back for more.
Mourinho is the exact opposite. He can't stay in the same place too long before he gets itchy feet and has to move on - usually after starting a war with the club/owner/press/fans. Can't deny that his record is outstanding and doesn't look like it's going to deteriorate. He can pick up a team, motivate them, win things, and then move on. I can't think of many managers that can do that. I also appreciate the idea that he's breaking the mold of ex-players being managers, along with ex-protoge AVB. What's more, he didn't need big money at Porto. I don't think anyone seriously thinks that had Mourinho been at Man City with the same budget at Mancini, City wouldn't be better and heading in a different direction.
In his favour, Mourinho has more time to overtake Ferguson. Probably.