Why is warm water comfortable, but warm air uncomfortable?
You constantly generate heat from metabolism.  The ability of this heat to be transferred to your surroundings from your skin is tremendously different in air vs. water. This is known as thermal conductivity. 

The ability of water to remove heat from your skin is roughly 24 times that of air. See list of materials and their thermal conductivity rates here

In water of close to body temp, you can still bleed off heat to water. Your ability to do so in air that is close to body temperature is greatly reduced, so much so that in order to keep up, you sweat and increase the cooling ability through the evaporation of that sweat at temperatures well below 98.6F.