IN the years that you are looking at, both engines will work fine and get the job done. The difference is the chassis. Depending on what size coach you are looking at, the Workhorse chassis may be the P series or the W series. Both will have the 8.1GM engine but on the W series chassis will have the Allison transmission, which many prefer. The P series chassis had the GM transmission.
The Ford V-10 F53 chassis will all have the Ford transmissions, which will work fine but I don't believe the tow/haul mode came out until 2006. In 2004-5 Ford had the overdrive 4 speed which was discontinued in 2006.