On the whole, I would say that the Navy PBRs and the "brown-water navy" in general were important weapons that helped reduce the effectiveness of Vietcong guerrilla operations and supply networks in the delta. However, it is hard to argue that they were "effective" given the overall loss of the war and the role that these supply networks played in that loss.
Militarily, the PBRs were quite effective. They were formidable fighting platforms that were highly maneuverable and drew such little water that they could operate almost anywhere. Because of this, they were very useful in pursuing guerrillas and supplies on the water.
However, the problem was that it was not at all easy to find and interdict these guerrillas and the supplies. There was no way that the PBRs were going to be able to identify and stop every boat that was carrying supplies or guerrillas. Because the Vietcong used small craft carrying personnel and supplies in a very piecemeal fashion, it was extremely hard to stop any sort of a large percentage of what was being moved.
Overall, then, I would argue that the PBRs themselves were superb weapons but that the task they faced was too big and too difficult for them to be truly effective.