Enable or disable Night Shift via Terminal
There is also another method described here for making your Mac think that your external display is primary: Fixing Night Shift incompatibility with external monitors
FWIW, I had the same issue immediately upon upgrading to Sierra, and solved it by uninstalling the NVIDIA Web Driver (not the CUDA driver) as seen below.
This is on a 2014 MacBook Pro with the NVIDIA GeForce GT 750M 2048 MB graphics GPU.
