Hi,
I have found a Mini PCIe card with a uBlox GPS on that I have been able to "pull out" NMEA data from.
I got mine from ebay (mini pcie blox | eBay), and it was pretty cheap, but came without the antenna. I got one of those from an RC multi rotor (http://www.horizonhobby.com/products/gps-antenna-350-qx-BLH7806).
I haven't found the time to tweak the existing GPS Arduino code yet, but it should be relatively simple I think... it uses the USB port in the Mini PCIe socket and presents itself as a virtual serial port under linux.
Just an idea!
/Thomas