The .41 is much less common, like drinking imported beer rather than draft.
It comes down to this... do you prefer imported beer or Bud?
It is my belief that the slight difference in diameter of the bullet makes little difference in terms of killing power between the 41 and 44. But you can load or buy loads up to about 300 gr on the 44 mag, which you can't do with a 41 mag. If killing power for hunting big game is your measure, I would move above the 44 mag.
People say that the 41 mag is more ballistically efficient than the 44 mag. People also say that the 41 mag loads tend to be more accurate from load to load until you get into the 250gr size. The 41 is not a 44, but it just depends on what you intend to do with the gun. So, get the one that speaks to you as the previous poster said. The 41 mag speaks to me.