See I would say if you wish to do MCA and want to have a good career ahead then you can choose any of the two universities. But if you compare the scenario of placements and the curriculum then I would recommend you to go for NIT Karnataka over Manipal University. NIT Karnataka have a better curriculum of MCA compared to Manipal University. If you go to NIT's, it add value to your CV as well as you will get more opportunities to discover different fields of CSE  and thus you will have a better possibility of getting job with higher packages as compared to Manipal University. NIT karnataka have better median packages than that of MU.

To know more about NIT karnataka visit the link below:

https://www.careers360.com/university/national-institute-of-technology-karnataka-surathkal

To know more about Manipal University visit the link below:

https://www.careers360.com/colleges/manipal-institute-of-technology-manipal

To know more about MCA visit the link below:

https://www.careers360.com/courses/mca-master-of-computer-applications

I hope this answer helps. All the very best for your future endeavors!