I have never seen a fast 3000GT in my life, even back a few years ago when they were out at the races in abundance....I would pick a SRT-4. When I was buying my LT1 Camaro 5 years ago I test drove the VR4, it was light years slower with its claimed 35hp advantage.
*edit*
If your talking about a regular Neon and a non-turbo 3000gt, it doesnt really matter, your talking about 2 cars not worth modding at all.