For helicopters, you have to rely on rocket launchers. They are spread around the map.
As for person bosses, I can't really say. I only put my points into the Assault Rifle to do some real damage. Also, you often need to pick enemies up from afar, so pistols might not be best suited for that.
I barely used my pistol with silencer, but unless you're not close up and aim for the head, it doesn't do much. But as I said, I only put 3 points into pistol.