Net, what if you have a really good cooler on the GPU and its only at 40c? Does that mean it produces less heat then a 50c CPU? If you are only looking at the temp, then you need to take how good the cooler is into account.
It will also depend on the CPU/GPU. I'm sure I could find a CPU that produces more heat then a low end GPU. But generally, when looking at the top of both CPUs and GPUs the GPU will produce more heat.