My 6th edition Hornady reloading manual shows the maximum velocity for a 250 gr. jhp at 850 fps out of a 45 Colt. The maximum velocity for a 240 gr. bullet out of the 44 mag. is shown at 1400 fps. Unless you are making some incredibly unsafe handloads, the 45 Colt will never beat the 44 mag. hands down.
That Hornady load is handicapped. I can push a cast 255 grain bullet over 900 fps out of my 45s, using Pyrodex or black powder. Besides, Hodgdon's load for strong 45 designs pushes a 240 grain Sierra JHC at 1532 fps from a 7.25" barrel, and it does it at a fraction of the operating pressures than the 44 mag works at.
The 45 Colt can be safely loaded to +P type loads in Rugers built on the large Blackhawk sized frame (not the new Vaqueros that just came out), Freedom Arms revolvers, T/C rifles and pistols, and the model '92 rifle, among others. John Linebaugh, and others, tested the Ruger Blackhawk to the point of destruction, and determined that it can safely handle loads that reach a maximum pressure that is 80% of a 44 magnum's max. That's because boring a 45 Colt hole in a cylinder leaves you with 80% of the steel that a 44 hole leaves on the outside edge of the cylinder. A custom 5-shot cylinder, with its massive walls, can handle higher pressures. 45 Colt brass, especially Starline brass, is plenty thick and strong enough to contain these pressures in a strong gun. Just cut one in half, and compare the brass to a halved 44 case.
The greater expansion ratio of the 45 caliber allows for comparable velocity at a lower pressure, given bullets of the same weight. That's why Hodgdon shows a +P 45 Colt load that propels a 360 grain cast bullet at 1167 fps, with only 29,800 CUP. Hodgdon's 44 mag load, fired from an inch longer barrel, gives you a 355 grain cast bullet at 1247 fps, but with a pressure of 37,900 CUP.
Once you allow for the differences between bullet weights, barrel length, and test guns, it's plain that a strong 45 Colt can chunk just as big a hunk of lead, just as fast, but with less muzzle blast than the 44 (do to the lower pressures). If you move up to the custom 5-shooters, the 45 leaves the 44 far behind, and it pokes a bigger hole to boot.