First, let me say that I am a die hard .45 Colt fan, owning 4 revolvers and a Marlin Cowboy rifle so chambered, but I would agree with Alyeska338 on this one, at least in comparing the two rifles I own using factory equivalent cartridges.
I purchased an original circa 1882 model '73 Winchester .44 W.C.F. (.44-40) about 3 years ago and have fired over 3,000 rounds to date. My .45 Colt Marlin cowboy rifle is 5 years old and I have several thousand rounds through it.
In comparing the accuracy of my Model '73 .44 W.C.F. (200-217 gr. bullets) against my .45 Colt Marlin Cowboy (250-265 gr. bullets) using factory equivalent hand loads at about 1,200 f.ps. , the '73 will, on the average, produce slightly smaller groups (about 1/2" smaller average @ 50 yards) than the .45.
However, when I shoot 325 - 350 gr. bullets in the .45, the groups will equal or better those of the .44.
A friend of mine who is an accomplished shooter and reloader, has a relatively new '92 Winchester in .45 Colt and was having a heck of a time getting good accuracy at 50 yards. Groups ran 4+" yards using several different 250 gr. bullets up to and including .456”. I gave him some .45 Colt's to try that were loaded with the RCBS 300 gr. bullet (320 grs. in w.w.) sized to .457" diameter over 20 grs. of 296. What a difference! The first group he fired with these cartridges went a little over 1" @ 50 yards for 5 shots from his rifle.
Mike Venturino has stated that on average, rifles chambered for the .44 W.C.F will give better accuracy than those chambered for .45 Colt but he was using 250 gr. bullets. Individual rifles are more accurate as some of you have stated. The heavier bullets do give an edge to the .45 colt for better accuracy in my experience.
I like both cartridges. The .44 W.C.F. is an historical lever action cartridge. That's what I like about it.
The .45 Colt, is also historical, but not in a rifle. In the Marlin Cowboy it becomes a miniature .45-70-350. That's what I like about it.
John