Measure up to an altitude of about 35 km (or 100,000 feet) is not easy. It is not simple even because there are no cheap barometers that can work in that temperature (down to -60 ° C) and pressure (close to 0 bar) range. So I have no choice but to rely on the GPS that is still usable to those altitudes if not blocked by the firmware. In short the GPS device manufacturers are required to comply with certain limits (in altitude and speed of the device) to prevent it from being used for example to guide arms. The manufacturers of commercial devices often include these limits without proper documentation or extensive test because devices will definitely used (except that in this case) on the earth.
A chipset that can be configured to operate at those altitudes, which has good performance and is cheap is the uBlox NEO-6M. On HobbyKing a GPS breakout board ready to use (with antenna and voltage regulator) cost just 15 Euros. To configure the chipset exists u-center a really complete tool for Windows that allows you to set the navigation mode to “Airborne”.
The connection is made through the MCU serial RX pin.