I have the same problem, but I fixed it. It seems that the vibration is from the shift knob that is getting a little loose on the shift lever. I fixed this by pulling the shift boot up (May have to remove the top of the console to get at the clips so you do not break them.), then taking about 3 zip ties and putting them around the base of the shift knob where the shift boot comes in contact with the knob. Pulled them very tight, then reseated the shift boot in the console. The zip ties will be under the shift boot and cannot be seen.
Try it, it works! Car is quiet now.
I love LS 5 speed questions!