Which is better, IIIT Pune for CSE or PEC for civil engineering?

It completely depends upon your interests. You should make up your mind about whether you connect with programming or Civil engineering. Choose the branch through which you can work for the field you want to work in.

My cousin has been a student of PEC University Chandigarh, civil engineering branch. According to his experience, apart from a few faculty members, the majority of the teachers don't care much whether the students understand the concepts involved in the curriculum or not. The placements for PEC University are also below average for the department of Civil Engineering. Around 3-4 reputed core companies visit the campus of the University for recruitment purposes.

However, technical, as well as cultural clubs present in the College, are very good and the environment that the college provides is also quite competitive. You will get the opportunity to learn many things both including those concerned with cultural as well as technical fields with the help of these clubs.

Here is a brief comparison of both institutes.

It will be better if you do your own research on the institutes, before making any decisions. There are many websites including the official websites of these colleges which can help you in making an appropriate decision for your career.