Matamata turtles are a very unique species given their ability to herd fish into shallow pools were they can capture their prey. So Russell, to capture Matamata turtles "unique" up on them!
Based on the work of researchers I know personally who capture turtles of different species, you will most likely need a snorkeler. The snorkeler will have to frequent areas where matamata turtles are found and creep up on the turtle extremely slowly once it's spotted. Once the snorkeler gets close enough it's a mad dash to catch the turtle before it's spooked. This works when the turtles are basking, and I'm not sure how often matamata turtles bask, so the technique may need to be modified.
Russ... I would recommend using fyke nets (a la Dick Vogt; see photo below with terrapin inside net). Most active turtles that are not attracted to baited traps can be caught in fyke nets. I have had good success with Malaclemys and Graptemys using this technique, and both of these are notorious for not going to baited traps. Because Matamatas are bottom walkers, you would want to ensure the "weighted line" of your lead net contacts the bottom substrate. If not, they will walk under your lead net. Let me know if you have any questions; I would be happy to chat further with you about it.
Will: I have used fyke nets before (E.S.George Reserve, a million years ago) so i know what you're talking about. It might work on matamatas, i also think baited traps might work. I was hoping to hear from someone who had actually caught matas so i could skip the "trying a number of things and hoping one might work" phase.