It doesn't matter if you are swimming or running. Its the temperature of your surrounding enviroment that determines how well your body can remove the access heat. Its alot easier to swim in a pool that is 78 degrees than a pool that is 85 degrees. After a few minutes swimming in an 85 degree pool will feel like you are swimming in a hot tub. The warm water sucks the energy out of you. 78 degrees ( the temp of most pools ) is not cold enough after a few minutes.
Also I can tell you from personal experience that my body's temp stays elevated long after I get out of the pool. The fact remains that swimming is not the most efficient way to burn caloires. Your biggest muscles in your legs, are simply dragged behind you when you swim, and starts and flip turns are not significant in burning calories
To prove my point once and for all. Which burns more calories? Lat Pull downs for an hour ( swimming ), or Squats for an hour( running ). Just because its painful or uncomfortable, doesn't mean you are burning alot of calories, it just means your body is not built to efficiently do the activity at hand.
If you want to burn the maximum calories stick to the stair machine.