Federal Communications Commission 22.925
Per FCC 22.925, using a cellphone on any aircraft, including weather balloons, is illegal unless the vehicle is touching the ground. Technically you could use a cellphone tracker on a weather balloon, but you would have to make sure that it stayed in airplane mode until the payload was on the ground. It may be possible to find an app that turns your phone's airplane mode off after a set number of hours. Unfortunately your phone is most likely going to die from extreme cold. Even if it does survive the extreme environment, you still risk having your phone land in an area with little or no coverage, especially considering your phone will by lying on the ground where reception is even lower than at head level.
The following is up to date as of July 15th 2015:
Cellular telephones installed in or carried aboard airplanes, balloons or any other type of aircraft must not be operated while such aircraft are airborne (not touching the ground). When any aircraft leaves the ground, all cellular telephones on board that aircraft must be turned off. The following notice must be posted on or near each cellular telephone installed in any aircraft:
“The use of cellular telephones while this aircraft is airborne is prohibited by FCC rules, and the violation of this rule could result in suspension of service and/or a fine. The use of cellular telephones while this aircraft is on the ground is subject to FAA regulations.”
If you would like to access the FCC regulation directly on their website, click here.