Both are great cars....although the 99's got more bad press because of the little issue. Still, I would go with the 01. Better seats, radio, a "Cobra" rear bumper, smoked headlights, and polished wheels.
If you were to buy these mods for the 99 Cobra to get it up to par, it would cost you at LEAST $2,000....
EDIT: Oh, they also have 31 spline axles instead of 28 spline. So add another $800 to get the 99 Cobra up to 01 specs.
As for transmissions...the 99's came with the T45 and the 01's got the T3650. Both have their own "weaknesses" so it's kind of a wash in my opinion.