Most would probably say get a Cobra, and in most cases, I do believe that is the more economical choice. For one, a terminator is more than just another blown mustang. We all know it has a blown/forged 4V motor, but it also have a better interior, better tranny, exterior, IRS (if that is your thing), etc.
In my case, I always wanted my GT to be like many of the built ones I've seen at MPH, and every time I went there I wanted it even more badly. Since I already have exterior and interior mods, and just about everything else, including a tranny that can support the added power, I figured building my GT is the way to go.
You'll also have to ask yourself is this a car you plan on sticking with for a long time? If value and name is important, I'd recommend the Cobra. In my situation, I knew I'd never want to sell my GT, so value really wasn't all that important. Plus sentimental value played a role. I started off with a constipated TURD, dyno'd only 205rwhp bone stock (it was an auto), and actually more than tripled its power.