Mine does it all the time and it's the plastic trim pieces on the roof panel frame - you get the same creaking noise if you just push it with your finger.
I first mentioned this to the dealer at the 10k service (now done 42k) but it's still there. They said they couldn't find a problem - useless gits.
Still, at least it fits with the creaking passenger seat (driver's seat has stopped now), creaking driver's door trim and creaking roof lining (fixed that myself cos it was the most irritating).
JD Power?, great dealers?, build quality? - I'm not convinced; hope you're reading this, Lexus GB.