From what I've read, a three-bladed prop is not as efficient as a two-blader. There is one more blade to cause drag, it is heavier and you should reduce either the diameter or the pitch compared to the recommended two-blade prop you are replacing. There's also one more blade to balance!
Unless it is for pure aesthetic reasons, (looks cool), or scale competition, I would use the two-bladed prop recommended by the engine manufacturer.

Jesse