The 45 Colt will outdo a 44 Mag if loaded accordingly. Modern brass 45 Colt brass is just as strong as 44 Mag brass, and the 45 Colt can shoot the same weigt bullet slightly faster than the 44 Mag at the same pressure - and heavier bullets (~350 grs) if you wish.
The only reason why the 44 Mag seems superior (to those who look only at load tables), is that all of the strong revolvers, and none of the weaker designs are chambered for it, while 45 Colt is chambered primarily in older, weaker designs such as 1873 SAA's.