Most body heat is generated in the deep organs of the body – especially the liver, brain, and heart, and in contraction of skeletal muscles. This is presumably because a) those organs are cannot easily lose the heat they generate to their surroundings (unlike, say, your skin), and b) they are working hard and generating excess energy.
The head is certainly warm, though:
Although it is apparently a myth that humans lose most of their heat through the head:
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