If I had both sitting in front of me and said pick one I would have one hell of a choice. Each have its pros and cons equally and it comes down to owner preference.
LS1 350 N/A VS 4.6 32V Supercharged
Both Rear Wheel Drive
M6 or Auto VS only M6
Leather or Cloth vs Leather w/suede inserts
Both have premium stereos but with exhaust who the hell cares right?
T-Tops vs nothing
made for 4 years vs 2 years
in 3 cars if you include gto vs only 1 car
Both have various colors
both have big aftermarkets
So in conclusion both have their pros and cons and quiet honestly I would probably pick a 04 Terminator. The LS1 was offered in the Camaro SS, Camaro z28, 04 GTO, Firebird Formula, T/A, and WS6. So in real fact the Cobra is a rarer car if you break it down. Who the hell cares if Ford wanted to slap a supercharger on the 4.6? What man doesnt like the sound of a supercharger coming from the car? Each car could go faster with more money of course if thats what your into then go for it I say but me I prefer to keep it mild and just have a great looking car personally. The cobra look sick as hell from front or behind especially with some nice wide tires in the back and the right set of rims but that goes for both personally. The 98-02 camaros are a great looking car also. I love the camaros with the center mount exhaust just freaking killer IMO. I would not buy a z28 or a formula. The WS6 is sick as well with the ram air hood and flip down headlights makes it a sinful looking car as well.