There's no point in bothering the FCC. They control station licenses, not networks. And since it was a live event controlled by the NFL and Viacom, the stations had no clue what was going to happen and would not be held accountable even if the FCC determined it was somehow a violation of their indecency rules ... which I doubt they would anyway, since the nipple was covered and thus technically not nudity.
I suppose you could file complaints with the FCC specifically asking for them to take action against the TV stations owned by Viacom that did air the Super Bowl, but even then the chances of action are so close to zero that it's probably not worth your time.
If you're upset about it, take it up with the NFL and the companies that advertised on the Super Bowl. They don't like dealing with annoyed customers threatening to stop using their products, so if enough people were to complain to them (again, highly unlikely, but you never know), they would take it up with Viacom, and Viacom is more likely to listen to the people that give them money.