If you take my opinion then opting for IIT Gandhinagar for CSE is a better choice than going for ECE at IIT Guwahati. I am a student of IIT Gandhinagar and I can say that the CSE department is one of the best departments in terms of curriculums and placements.
I am assuming that you are asking this question after the first round of seat allocations are announced. If you are confused between IIT Gandhinagar CSE and IIT Guwahati ECE, consider the following points:
Both the colleges will provide a good learning environment and ample opportunities so go for the one that aligns with your interests the most.