I usually know the rules pretty well, but am a bit unsure about this.
 The temperature of the pots are not the same.
 The temperatures of the pots are not the same.
 The temperature of the pots is not the same.
I think it should be  as  doesn't sound proper. I suppose  could be proper, but it sounds the strangest.
Another reason I think it should be  is that  should refer to the situation in which there are multiple items in each of the prepositional objects
The potatoes in the pots were not cooked properly. <- there are multiple potatoes in each pot, where as there is only one temperature for each pot.