Okay, here's the deal: after trying the things suggested, I discovered that water wasn't getting to the third floor radiators. I called in an HVAC technician who's here now. He drained my expansion tank, is putting in some new pipes (the pipe that is used to fill the system is old and corroded), and installing a new pressure relief valve. Hopefully the bill won't be too painful, but at least, I'll have heat to the third floor and no more thumping!

Again, thanks to all of you who contributed ideas. I know where to go with any other house related problems in the future.