According, to careers 360 VNIT has AAAA rating which means very good and Manipal has AAAA+ rating which means outstanding.

Ratings are based on Placements, Faculty, Cut-offs of national / state level Entrance exams, Accreditation and Reward status and Publication record from Elsevier’s indexing database - Scopus.

In NIRF, VNIT is in 42 position and Manipal is in 43 position. 

Both the institutes are good it totally depends on your choice which college you prefer.

Good Luck!!