Should I join IGDTUW Delhi mechanical and automation, or PEC Chandigarh civil branch? Which is better?

Both IGDTUW Delhi and PEC Chandigarh are reputed colleges and are equally good but both these courses are very different from each other. 

If you are interested in higher studies and want to do M.Tech or Ph.D., then only opt for PEC civil. The pressure for studies would be less. You also have no restrictions in doing extracurricular activities. Here you can focus on other things besides studies, like on your hobbies or learning and developing a new skill or a new language which can be helpful in your career. 

Here’s a brief overview of the courses mentioned in the question. 

Hope this answer clears some of your doubts.