But they really aren't in the same class. Z3's are tourers, not sports cars per se'. But then again, MX-5's are roadsters, not sports cars in the practical sense. They don't exist in the same market bracket and fulfil entirely different ownership purposes :)
My personal opinion however, after finally settling on a NA mx-5 for my weekend race car, is that the mx-5 is honestly one of the best bang-for-buck circuit cars you can get. With only ~$10k invested in mine, it happily outpaces cars 6-10x the value.
The trouble with this sort of thing is, if you're going to remove practicality and low cost from the equation when making your "best sports car" assessment, you're competing against every sports car ever made by Ferrari, Porsche, Jaguar, etc. on their own terms. Pretty much all the reasons why you'd say a Z3 is a better sports car than, say, a Jaguar E-Type involve practicality and cost, I would think.
I was responding mostly to the absolute statement "best two seater sports car ever made". I think the Miata is a great car, probably the best intro sports car if you are into grassroots racing or similar hobbyist activities, but I'd take the Z3 over it for most purposes.