Why do I hear a swishing sound when I apply my breaks?

You sure it is not brakes? Or maybe it is breaks? Choose one. Could your brake (break) booster be leaking vacuum and hissing?

As Bob says, could well be the booster, which is located on the firewall directly opposite the driver's knees...where he feels the sound originates. Check it with another person. Engine running, stopped in park, e-brake on : use a foot or 2 of approx. 1 in. diameter rubber hose as a stethoscope. Apply the brake pedal fully down, the other person listening all around the booster, the hose connections, etc., while pumping the pedal at a calm, regular pace. Hear escaping air? It would be odd for the one who test drove the truck with your new master cylinder too have NOT noticed an unusual sound when braking. But, never can tell until you check it yourself. MAYBE you're hearing the perfectly normal sound of the air pressure assist during a stop. Good luck man. (If the brakes are functioning as they should, I wouldn't sweat it...but you DO want to be sure with such a critical system.)