What should I prefer GEC Goa CSE or EEE in NIT Goa?

The preference should be firstly based on the branch and not on the colleges. Opt for the college where you get the branch of your choice. It's not college that matters but rather it's the branch. If you get the branch of your choice, you will be more likely to study that well and attain a successful future. 

• If you are more into the programming languages, the technology and are passionate about learning the subjects associated with the CSE, then opt for GEC as there's nothing above the branch. 
• If you have an interest in EEE, opt straight for the NIT Goa as it is an institute that will never disappoint in terms of placement, academics, faculties, or higher studies. 
• NIT Goa is a brand in itself. But opt for it only if you are sure about the branch.

If you think that you will take EEE in NIT Goa and then change the branch to CSE, then it's nearly impossible. There are high cut offs for changing the branch and it happens after following a certain set of rules that is not possible. So choose wisely as your career depends on it.