I was in the same place a couple years ago, didnt matter what kind of dealership it was, all the GX and LX's were above market value. I did eventually find a 2007 GX470 with Sport package and warranty at Stevinson Lexus in Lakewood, it wasnt marked up from any of the others so I felt like I got a good deal on a very low mile and unique GX. I have no regrets from moving up from my 2003 4Runner Sport V8.
You might have better luck with private sellers, another idea is check the non metro area Lexus dealers, I have one in Colorado Springs near me.
//Anders