I am biased, but with the GT you get OBD2 and EECV. Both make it a pain in the behind to hop up.
You also get an engine that only lasted 13 years, from the '91 crown victoria to the '04 mustang. The 5.0/302 lasted from the '64 mustang to whenever they stoped putting it in the explorer. The only changes along the way were the rear main seal, roller lifters, pedestal rockers, fuel injection, serpentine belt and stroke. Those are minor details. The two valve 4.6 has two incompatible cylinder heads already; the 91-98, and the PI.
In ten years, you will still be able to get everything for a 5.0, but the two valve 4.6 will have very little support. You will have to transplant a 3 valve to use available speed parts. That probably won't be very difficult, but it's one more step and one more expense to deal with.
Also, if the owner already has a '95 Cobra, why does he need a '94?
It's because the '94 has already finished depretiating and the GT is still going down. He is trying to pull money out of his GT while he still can. If he waits a few more years, the price of your cobra will be higher than his GT and he would be the one paying.
Stick with the cobra, it is a new classic, it was made only 2 years with the 5.0 in the SN95 body. It's the '65.5 fastback GT K code of it's day, a car that demands triple the price of a nice V8 coupe. The Cobra is allready worth about 50% more than a GT, so it is well on it's way.