Hmm, maybe you could try jacking up each side of the car, and spinning the wheel? See if any sounds happen then, if it does, inspect it further, sometimes it could be a foreign object stuck somewhere.
I remember back in the dealership where I worked, we spent ages looking for a weird noise and it turned out to be a bit of card stuck between the caliper/carrier!
EDIT: But if its a knocking noise, may be something else, (not sure about the IS300H), but some brake discs have a screws to secure it, make sure they're tightened up correctly, and check the anti squeal shields are ok? And make sure the wheel bolts are torqued/tightened correctly.
Or just go back to the dealer an ask to drive another 300H and see if it is present on another car too