1997 Mercury Sable problem when using brakes

If the car is at a speed of 25 or more when the brakes are used there is a thumping sound coming from the front as though the brakes are bad or the tire is going flat or has a bubble that is rubbing on a spoke. We have changed the brake pads, the rotors are in very good shape, and put new tires on the front.The sound is softer but still happens. We don't know if it could be the emergency brake is stuck, the car needs an alignment or something in an area we haven't worked on before. The car stops well and we do not want to damage something more than it already is.