I can imagine how you feel. My 03 is my newest and by far, most expensive vehicle. Even my '86 4Runner has no cracks around the windows (they used metal back then, plus the windows are the sliding type like on the 80 series). No cracks on my '01 honda, either. I'm surprised a '06 would have cracks. That should be covered under the new car warranty (at least the lexus new car warranty [4 yr/50K mi] covers everything short of paint chips from rocks). The problem is you run the risk of a tech pulling the upper and lower inner quarter body panels to replace the window, and that means possible creaks that weren't there before. You'd think Toyota would have improved the QC on their flagship vehicle and used aluminum instead of plastic! Would have only cost maybe $50/vehicle for all the windows.
Well I looked again tonight (been a very cold week here) and my passenger side is cracked as well. Looks like a straight split as if it was the way it was designed. But we know its a defect. Unreal.