No question that the .44 mag would be better. You can easily take deer out to 125 yards. You can buy factory ammo in a wide varity of loads. Your instincts are correct, in that it is roughly equivalent to your muzzle loader shooting a .44 mag sabot with a 100 grain charge.
The 20 gauge sheds velocity much quicker, and in general terms, a shotgun slug, even out of a rifled shotgun barrel, is almost never as accurate as a good rifle. The shotgun shells with slugs are way more expensive than the .44 mag rounds.
The slug just doesn't "give you anything" in comparison to the rifle round, except for more recoil, less accuracy, higher price, and lower velocity out at 100 yards or more.