the 01 might have aluminum block, but the 03 has iron cause it has to be stronger to handle all that power. plus it has forged internals for strength and durability. go for the 03 or 04, it would be the wiser choice
As to answer the question who would win, probably the 01 Cobra. But the question by itself is way too vague. What mods does each car have? What kind of supercharger is the 01 running? Intercooled? How much boost?
Take a stock 03 Cobra and a stock 01 Cobra w/a Vortech kit @7psi, and given good traction, the 01 would win in the quarter. That's my opinion.
Depending on what supercharger... if you stick a stock eaton on the 01 with an intercooler... maybe... more or less it would depend on the lane conditions and driver...
But, you can run more boost on the 03 due to the massive internals... and the 03 will last much, much longer... Get an 03/04... your investment will be much more worth it.
If you just theoretically suppose that a supercharged 01 and a factory blown 03 were making the same horsepower and torque, then the 01 would have the advantage in curb weight. I also think that the 01 might have a slightly better initial torque multiplication from the gearing, but of course the T-56 probably would hold its RPMs better. I'd bet with similiar traction, the 01 would be a few ticks quicker. When you consider the possible lack of longevity of the 01 and the factory warranty of the 03, the difference would seem hardly worth it.
How great it would have been to have an all-aluminum engine with the weight of the 01 with the factory-backed horsepower numbers of the 03! The more neutral weight bias of the 01 mixed with the power of the 03 would probably had the Corvette guys really sweating it out...on the strip or road course.