S2000 I think is a better buy unless you buy a brand new Miata.
S2000 has the better motor, however the NC Miata has better brakes.
Compared to the NA/NB miata, unless you can find one that for less than 5000, youd spend close to what you would pay for to get a 2000-2001 S2000 equal performance wise.
Here is what I would consider doing to the miata to make it as fast as the S2000:
Forced Induction, Super/Turbo... with a safe boost and tune to get around 180hp
Full Suspension
Wider Wheels/Good Tires
Chassis Brace
Roll Bar (gotta have it, S2000 stock)
upgrade the pads/fluids/stainless steel lines
Sway bars
Once you do that, you have something as quick or quicker than a stock S2000.
However the Miata's cheaper to insure, cheaper to fix, and will wear out parts less frequently than the S2000 due to its lighter weight.
I like the fit and finish on the S2000 but hate having to pay for it on the insurance.
Now with the NC miata, that's a whole new ball game. It's a better platform than the S2000 and only lacks the motor. I like how you can get the folding hard top or a removable hard top as well.