The simplest difference is that a wireway is a raceway and cable tray is not.
Here is the definitions of each item from the 2008 NEC:
Cable Tray System. A unit or assembly of units or sections and associated fittings forming a structural system used to securely fasten or support cables and raceways.
Metal Wireways. Sheet metal troughs with hinged or removable covers for housing and protecting electrical wires and cable and in which conductors are laid in place after the wireway has been installed as a complete system.
Chris