It's a sensor is going to be attached to a person while running or performing labor intensive tasks. So what you're saying is that it's kind of impossible to find the "best" kind of sensor? What would be the "best," relatively speaking? IR? IC's dedicated to temp sensing?
What do you want to use the data for?
Monitoring of the testperson's temperature
during the task so that he may rest at an appropriate time?
Or adding it to other data
after the task for some research purpose?
For the latter the temperature logging pill would do.
How feasable is it to transmit a signal (radio or sound) out of the body from the intestinal tract?
If you could add a transmitter in the temperaturesensing pill then it can send the temperature reading without needing wires.
Kinda like this:
https://spinoff.nasa.gov/Spinoff2006/hm_1.html