did it just start knocking out of the blue? if it just happened for no reason and it still runs great i'll bet the flexplate is cracked. they like to crack around the bolt holes and then knock against the torque converter and engine block. sounds exactly like a rod knocking.
that is if it's an auto of course. rod knocks tend to creep up and get worse over time as the wrist pins in the pistons wear out, or come on all at once when a rod gets bent usualy from hyrdo-locking the engine.