As far as Ruger single actions are concerned, the .41 Mag is available only in the Blackhawk configuration with 6 1/2" barrel (or 4 5/8") while the .44 Mag is offered as the Super Blackhawk with 7 1/2" barrel with the Super Blackhawk "Dragoon" style grip frame.
As the Bisley, I don't think there is any difference, except the .41 Bisley is very scarce.
Of course all of the above is meaningless if you go the custom sixgun route.
But as to which cartridge, it's a toss up. The .44 will handle very heavey bullets (300 grs. or so) better, but when do you realley need 300 gr. bullets?