would air in the water pump line make a sound like someone knocking on a door?

Most likely Not, No. The noise im betting your hearing is your fan running into something.

Nope, not going to be in the cooling system. Check all your fluids and pay special attention to the plastic fan. Make sure it is not rubbing or missing blades. We are the large BMW shop in Vallejo. I already replied to the fog light question. Call Adrian at Milt's Service Garage for more info (707)643-7548

What you are discribing is anything from a rod or crank bearing problem to a broken exhaust mount. Take it in and have it checked.