It all really depends what you're looking for in the car. The L05 is going to be cheaper to maintain, there are things you can do to up its output (throttle body spacer, exhaust improvements; if you're really serious - Vortec heads, LT1 cam, etc). The L99 you can tune via laptop, the L05 you have to buy a tuned PROM chip.
Personally, I'd make my decision based on which car is better taken care of. Performance wise, the torque and horsepower output is about equal in stock trim. If one seems neglected and 'ragged out', move on, because it'll probably crap out on you.
The '93 (and all '91 to '93 B-cars) has a 700R4 transmission, sometimes referred to as the 4L60. It's a 'dumb' tranny, in that it operates based just on mechanical means. From '94 up, all B-cars got 4L60E trannys, where the PCM has a say in how they operate.