So if you load a .41 Magnum for bear will it shoot flatter than a .357 or a .44 Magnum loaded for bear??? Just kidding, COR, just kidding.
Back to the main topic: does a .41 Magnum shoot flatter than a .357 or a .44 Magnum? Yes it does, according to reloading charts for the .41 Magnum that I googled, and I used that in part in deciding to get the .41 Magnum. The velocity advantage becomes moreso as barrel length increases, so if you are going to shoot a 7 1/2 inch barrel or longer, you can obtain the velocity advantage over .44 Mag reloads and I would presume over the .357 Mag as well, but I did not compare the .41 to the .357 Mag as I was choosing between the .41 and .44 mags. If I remember correctly, there were several loadings to get the 210 grainer over 1626 fps or faster, and possibly close to or over 1700 fps. What I will do if you are still researching this is find the link for the .41 Mag loadings for you and post it here.
However, if you are the kind of guy that likes the 4 5/8 inch barrel guns which are great for carry, then you will get more performance out of the .44 Mag with its heavier bullets. An observation I have made over the years, especially with rifles ( and it seems to carry over to hand guns as well) is that when you shorten the barrel length you loose more efficiency (Kinetic Energy, velocity, and I know how the 2 are related) with lighter bullets than you do with heavier bullets, for a given caliber. And the .44 Mag and .41 Mag, while not the same, are similar, or rather the .44 is only 19/1,000's more caliber, and has a slightly higher case capacity. If you want max killing power ( or penetration rather), Garrett Cartridges offers some very stout .44 mag loads with 310 gr and 330 grain bullets. You can go to Garrettcartridges.com and read up on them, just click on .44 magum. But read all his articles on penetration. I think he is spot on, but has a little bias in comparing the 45-70 to the .458 Win Mag (didn't use the same bullet in testing the 458 that he used in his 45-70 testing). Garrett does not offer loads in .41 Magnum, not currently. I think he should. His Hammerhead bullets have a very high sectional density for a pistol bullet, and they are "more weight forward" which aids in penetration and allowing the bullet to "go straighter when they hit flesh/bone without turning sideways".
I met a guy at the gun shop where I picked up my Ruger Super Blackhawk Hunter in .41 Mag, a Distributor Exclusive, and hurry if you want one, as there are only 33 are left, and they have everything on them you could want including SS, smooth cylinder, good looking dark wood laminate grips, 7.5 inch barrel, and a solid rib across the top of the barrel and it's grooved for scope rings, which come with the gun. Ok, so the guy I met there had hunted deer with a handgun over 20 yrs and is from the northeast (bigger deer than FLA) and he loaded 170 gr bullet to 1700 fps in his .41 Mag for deer. He said he never had to hit one more than once and got all the penetration he could want from any angle. He had a 7.5 inch barreled gun, and I am pretty sure it was a Blackhawk of some kind. So if you shoot factory ammo, I guess there is not much difference, but if you reload, you will notice a difference with the 210 grainers in .41 compared to the 240 grainers in .44 Mag. Caveat: you can load the 180 grainers in .44 Mag to comparable velocities to the 170 grainer in .41 Mag.
I hope this was useful, and check out Garrett Cartridges, if nothing else, for the info on penetration and how to get it.