I have priced interiors at both of these(and a few others) in the past myself. The difference between the two prices for these shops is that the Aero Comfort pricing includes all options such as the control wheel leather wrap, glareshield upholstery, and other items while the Las Cruces shop has a base price for the interior and you have to add on the other items as you go. Basically the $6500 price goes up considerably if you want to include the items that are included in the competing shop's interior package.
My recommendation is to make sure that you look at the quality, materials, and design options and compare apples to apples before you choose any particular shop. Last but not least do what you are doing now which is ask the Mooneyspace team about their experiences with any of these shops.