I am using a USB GPS to keep the TTL serial port on the Raspberry Pi free, plus you have more options to buy with a USB port. 

Different companies do the GPS differently.  A GPS based on the U-Blox chip set is usually defaulted to vehicle mode. But the U-Blox Windows software can configure it for airplane mode which is good for 50,000 meters. If I remember correctly there are three Aircraft modes. Use the one with the least dynamic movement, which is the closest to a balloon. 

The other advantage of a USB version is it is easier to configure with a Windows computer, just plug it in. 

I have seen a subroutine on the internet you can use to send the proper binary string to convert a U-Blox chipset to go to USB mode. But I have not tried it. It is written in C but could be easily converted to python for a Raspberry Pi TTL or USB.

I just bought a $12.30 USB GPS with the U-Blox 7020 chipset. I have not connected it to a Raspberry Pi yet, but hope to this week.