Firstly, in the event of the body needing energy for stuff like digestion or growing, the body generally diverts blood away from the limbs towards the "core", where the real work's being done by the heart and stomach, and to the brain.
This is especially common in newborns, as their limbs are basically useless until they're mobile, while pretty much 99% of their daily activities are growing and digesting. At the same time, their brain is doing an awful lot of growing and "re-wiring" in preparation for useful tasks, such as getting your attention and being cute on demand.
The general recommendation I've found is to check the heat of the back of the neck (path from heart to brain) and heat of the torso (contains everything else).
Also be aware that any uncovered part of the body will get cold faster than any covered part, especially the "sticky-out" bits (hands, feet, ears, etc.), because that's where the heat can get out from. So if your baby's hands seem worryingly cold, mittens would be the first step (Also, adorable!). But you should only really be doing this if you're out somewhere cold, or if your baby seems uncomfortable, as you're effectively blocking off the avenues of release for excess heat from the internal organs.
One source is here, but most of the sources when googling "baby's hands cold" say the same.