Hello Jason,
I just checked the Matlab web page and you can call DLLs from MEX files. When you install the imaq driver, a DLL will be placed in your system directory and if you install the C libraries, this will have a lib which will allow you to call the functions directly from the DLL. There are also examples that come with the driver to illustrate how you would acquire images and shows you how to get the 2-D array of pixels back. We also have software you can buy to do advanced processing, but it sounds like you want to handle this yourself (just wanted to make you aware of it).
Here's the link I found that describes how to call DLLs from Matlab
http://www.mathworks.com/support/solutions/data/10702.shtml
Hope this helps,
Brad Buchanan
Product Support Engineer
National
Instruments