I've owned both cars, raced both cars and heavily modified both cars.
Technology - Bar none, the coyote takes the cake. More features hands down.
Handling - The coyote has a better chassis, better and more developed suspension and brakes. Coyote takes the win here.
Performance - On a road course, the coyote will most likely take the win. At a dragstrip, stock for stock it is a drivers race. Mod for Mod, up until the Cobra swaps blowers, it comes down to the dailing in of the car and the driver. However, the Cobra makes a lot of power with very little money invested.
I'll be honest and say to this day, I miss my Cobra. The presence, the sheer torque of the car and the sound it made were all amazing. However, every time I get into my '14, I have a huge shit eating grin on my face because of how nice the car is and knowing what it is capable of.
Consensus - You cannot go wrong with either car. It is going to come down to what you can afford, what you prefer when it comes to comfort, features, options, and what you want out of the car.
Before buying a Cobra, check SVTP and make sure you have it inspect, compression tests done. Contact Robert @ Hi-End Auto out of VA. I bought my Mach 1 from him and he specializes in 03/04 Cobra's. He won't sell you a turd and you'll get a good deal on one. If there is a problem with a car he has, you will know what is done to it and what the issues, if any are. That is your best route buying one. Private party is sketchy because people want to move Cobra's and typically don't declare every defect or problem.
Good luck OP.