Both are the decent college. There will be the fees difference, University of Kerala has less fees structure than Amritha so you can choose as per your convenience. Amrita Vishwa Vidyapeetham is a multi-campus, multi-disciplinary research academia that is accredited 'A' by NAAC and is ranked as one of the best research institutions in India. University of Kerala is the best University in the state (Chancellors Award for Best University in the state). The colleges help the students of academic excellence through holistic education and development of right skills.

Good Luck!