Look at the Moog Problem Solver upper control arms. They will be your best option for a stock replacement, far superior to any other stock replacement option aside from Mopar.
MOOG CK620188 is the part number. They are about $75 each before shipping @ RockAuto.com
However, given that you are lifted, it is possible that you may be pushing the limits of the factory upper control arm for getting a decent alignment. I know when my factory stock ball joints were still good, my Commander was not going to hit factory alignment specs with the lift....
With that in mind, my set of JBA Uppers will be here on Tuesday.
2007 Commander 4.7
265/70/17 Falken AT2, 17x9" Level 8 - Strike 5
RC Lift, Bilstein Struts, JBA 6.7s, Monroe LL's
AEM Intake, SuperChips Flashpaq