Oh, boy (or in this case, oh, girl), you really don't want either of these guys to be your dad! Both did some pretty heinous stuff to their respective daughters, and neither can really claim the moral high ground in any way.
Handsome Jack really only imprisoned and sacrificed his daughter the one time, though, while Booker DeWitt just keeps. on. doing. it. in. every. single. reality. Elizabeth gets him back though, killing him off in universe after universe.
In a knock down, drag out fight, who would come out ahead? It's a tough one -- Booker can swap between realities to get the upper hand and find a universe where he has the advantage. But Handsome Jack does have a whole lot of firepower on his side, from the entirety of Hyperion Corporation to potentially controlling the world-destroying Warrior after opening the vault.
If Jack gets his pet Warrior, the win goes to him (unless Songbird constantly shows up to thwart the Warrior), otherwise I see the grim-faced DeWitt coming out the victor and then probably learning some other devastating truth about his past to make him even more hard boiled than before.