The 5th gen's are slightly lighter, while the 6th gen has a very slightly larger front sway bar (depending on the model and it's only by a couple mm). Unless you get a 6th gen Si which has a 26mm front sway bar as opposed to 19mm (5th gen) or 21mm (6th gen Non-Si). Some of the 5th gen EX sedans were equipped with 13mm rear sway bars which provide improved handling. The 99-00 Si comes with one stock.
It's really up to you. If I had to guess, stock vs. stock and if both were equipped with the same parts, they probably handle the same. But the 5th gen MAY come out on top being it's lighter.
