well how big are the pots? i had 3 plants that frew little pods in the same pot that did just fine, i do not have any experience with larger pepper plants in the same pot as i keep mine 1 per pot. BUT at the size yours are i would not suggest trying to separate them as the root system are already prbably tangled like a mofo and you may kill all three! so leave them and see what happens, this way you know what will happen with multiple plants in the same pot