Because the 997 followed the 996, you could argue that that is the better car because it benefits from more technology and improvements to the design.
Actually, I think it's the very opposite. The 996 is perhaps the last of the "driver's" 911. What I mean is; it has traction control (although on early 996's it was optional) and ABS of course, but the driver aids are generally less than the 997 and you still feel like you are driving the car. That's not to say the 997 s a bad car, it's not - far from it in fact.
Obviously this then opens a can of worms because some 911 fans will say that the 993 (the last of the aircooled 911's) is better than the 996 and 997.
Unfortunately therefore there is no definitive answer. It all depends on who you are and what you want.
My personal answer to your question is
What is the best: The 996.1 i.e. the very first of the 996.
Why: Coz it is ;)