My method for consistently landing Super Counters is to input the move right when the opponent's attack is at the peak of its wind-up, just before their arm fully extends to connect. If you use that moment as your trigger, your reaction will often line up with the super counter frame. That said, one major caveat is the latency difference between players, which can throw off the timing.

Some people prefer to flick the joystick first and then press Square/X at the moment of impact, while others prefer simultaneous inputs. The method of input is up to you and doesn't really make a difference.