when you replaced the knuckle(s), did you remember to crank the axle nut back to spec? I've forgotten to do that before and the same thudding occurs. But it really sounds like a bad ball joint could be your problem. Jack that corner of the car up and try wobbling the wheel. If there is any top to bottom movement, have someone else try wobbling it while you reach behind and feel the joint where it's making movement. If no joints are flexing, check to see if it looks like the wheel and brake rotor move when the knuckle doesn't.