As far as Arduino modules go, the Adafruit Ultimate GPS works well above the limits of weather balloons. From what I've read, Adafruit read the FCC documents differently and found that they could indeed go above the 60,000 ft cap most of the others stop at. It does require some programming but there are some great You Tube tutorials. Fairly cheap too. $40 should get you most everything needed.
Here is a great resource.