The 41 magnum is a bit milder than the .44 magnum to shoot. However it is harder to find factory loaded ammunition.
The .44 magnum is easy to find and in so many flavors you won't have any trouble finding a load that fits your purpose, target, plinking, hunting, etc.
The .45 is such a classic. In factory loads you will find plenty of suitable plinking rounds and even good target and defensive rounds. You could hunt with it as it is loaded but you don't really get the most out of this round unless you reload it up to take advantage of the Ruger strength.
That said, if 99% of your use is for fun, the .45 wins for me hands down. If you want to hunt and don't reload, you might find some custom loads that would take care of you, but you pay the price!
If I had to choose just one gun I would choose my Ruger .44 magnum over the .45 because I know I can find ammunition for it more easily. I can also load ammunition for the .44 to do anything I want. As nice as the .41 is, I would not choose it over the .44 or .45 for my only big bore handgun.