Dear applicant overall both of the above Medical Institutions are good for your higher education. But yes Kasturba Medical College is under Manipal Academy of Higher Education, and as per the NIRF Ranking of 2020 it was ranked 21st among all the medical colleges in India. So it would be wiser to choose KMC Mangalore for better career exposure, more progression of your curriculum too.

https://www.careers360.com/colleges/kasturba-medical-college-mangalore

Good luck!!!