One year ago my cousin from Ranchi was in the same dilemma. After consulting personally with a few students of BIT Mesra, he decided to join Jaypee Noida. This was because the students from BIT Mesra themselves suggested not to opt for BIT Mesra. Some of the reasons are:
You will be a graduate after four years, so always think of what will prove to be more advantageous to you after you graduate. Noida is growing rapidly. It is a hub of multinational companies, it will give you more exposure. Many students go on for MS courses, get good placements, etc., at Jaypee Institute of Information Technology. But, both the institutions were set up by industrialists.
It is important to remember that it is not always about the college, but about you. It is important to choose what interests you rather than a college with a better brand name.