That is a tough decision. I say test drive both and see which you like more.
If you are more than 6ft tall, you will be more comfortable in the new GT. I came so close to getting a Mach 1 in 03, but just couldn't push myself to get a car I don't really fit into. I was driving an hour each way to work and being comfortable was a priority.
The new GT will handle better, but a Cobra is still a Cobra, and a Terminator no less. Either way, Congrats.
If you get the cobra, I just hope it was hammered too bad by the last owner. (Or a flood car from NOLA) I had a buddy you got a Cobra stang (non-terminator) used and was having problems with the pass door window operations and fitment. When I went to fix it, the door was Blue on his red car and it was quite obvious the car had been t-boned. In other words, check the Cobra over real good.