This completely depends on your choice and preferences. The only thing you should take into account is how the course will benefit your career ahead.

• IIEST Shibpur and IISER Bhopal offer different career paths. 
• IIEST Shibpur is an engineering college and will push you most probably into a technical or corporate line. 
• IISER has a completely different approach. It focuses on scientific research and you will most probably end up in academia or research-oriented jobs.
• IIEST is a very old and reputed institute in the country and definitely, its placements will be better compared to IISER Bhopal.

This decision entirely depends on you. Choose which career path you want to avail yourself and work toward establishing it.