I was only attacked one time by super mutants and they spawned in the little marshy area by the tug boat (the one with the generator). At the time, I had only two or three settlers, three or 4 super mutant masters spawned (don't remember my level), one had a mingun, I circled around behind them while two junkyard dogs (Gene's dogs) kept them preoccupied enough for me to kill them. Prior to the attack, I was setting up some houses for future settlers when I heard one of the settlers shooting. Got out of workshop and ran around the house that I'd just built on the beach to see the mutants.
After the attack, I put up a rather high guard tower by the transmitter shed to overlook the entire island, I also installed a siren on the tower. I put turrents/guard houses on top of hills overlooking valleys all across the span of the island. I think I have at least 20 turrents spread across the island, I even have one mounted on the two boats that are partially sunk just off the beach.