Honestly speaking, both Thapar University and Manipal University are reputable institutions for a B.Tech in computer science. So the decision on which one is better for you ultimately depends on your personal preferences and priorities. is 

Thapar University is a highly esteemed, private engineering and technology university located in Patiala, India. Known for its strong academic programs and rich research culture in computer science, this university has it all. Additionally, it offers a range of student services, including career counseling and internships.

Manipal University, on the other hand, is a private university located in Manipal, India. It is one of the oldest and most established universities in the country and is known for its iRobot programs in CSE. The university has a number of student-driven bodies that promote extracurricular activities.

Some factors to consider while choosing between the two include 

• Proximity to hometown
• campus life
• Fees and other expenses 
• CSE Program offered

Both the colleges are almost similar in all aspects. So what actually matters is that if you live in the North, choose Thapar but if you are from the south choose Manipal. Both universities have the same fee and both are equally reputed private colleges after BITS. So I would suggest that whichever college is near your hometown go for it.

Ultimately, both universities are highly esteemed institutions and either one would be a decent choice for a B.Tech in computer science.