You could have suspension or other problems but I just fixed a squeak that occurred only with the top up by the following:
Begin lowering the roof and stop the process by letting go of the button while the roof is just setting down in the trunk. This leaves the raised covers pointing up vertically to let the roof pass. (When the roof is up these covers form the rear "package shelf".) In the center of the car just under this cover there is a round black rubber bumper stop the size of a 50 cent piece (whatever those are). This stop is adjustable up-and-down. Rotating it counterclockwise raises the stop and clockwise lowers it. I raised my rubber stop, by hand, a couple of turns upward.
For my SC that's all it took. The squeak is gone. This bumper helps to bind the package shelf to the roof when it is up and stops if from moving around - and squeaking. I don't know the Lexus method for adjusting this bumper stop but a turn or two worked for me. Good luck!
Hi there, I tried your method to turn the stop up as I have pretty much the same rattle on my SC430. The rattle stopped for a few days but came back again after I had my top down/up. Is there anything I can do about it? Thanks