In the thermal IR (used by radiant temp sensors), the zenith sky can appear to be less than -40C if the air is dry. Humidity and haze will increase this significantly.
Clouds can appear very cold at altitude (simply because it is cold up that high), but can be near ambient at low altitude.
ie, I don't think that there is a magic difference between ambient and sky that will tell you categorically if clouds are present. However, there are obviously proprietary strategies that can do a good job (eg for Boltwood). Maybe a good place to start would be to set the gear running in clear conditions and look for (say) a 10-15C increase in sky temperature (relative to ambient) to indicate cloud cover. That should account for the humidity on the night and give you a good chance of detecting cold high level clouds, as well as intermediate and low level stuff. You will probably also find that there is an absolute temperature, below which the sky will always be clear.
You will have probably have to experiment to see what works best with your sensor, since spectral response, zenith angle and acceptance angle will affect the results. Grateful if you could keep us informed of your findings - others will be interested.
ref:
http://journals.ametsoc.org/doi/pdf/...2007JAMC1615.1