Hello.
In terms of ranking Manipal University is good while they both universities are having same rating, fee structure for BTech mechatronics is higher in thapar University, overall the course is equivalent good in in both the universities but if you are expecting quite less fee then you should go with the Manipal University, for more detailed comparison you can go with the below link:
https://www.careers360.com/compare-colleges?college=282-174-course%3D13030-9317&google_id=106221245215279268132&gtoken=eyJhbGciOiJSUzI1NiIsImtpZCI6IjI4Yjc0MWU4ZGU5ODRhNDcxNTlmMTllNmQ3NzgzZTlkNGZhODEwZGIiLCJ0eXAiOiJKV1QifQ.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.orZTG9gF2DM4K_AtQIya-1HPrC7Uu2AD5cUGkpe3b8vD2sc4BGKMZMsnRJfvZQurx8jQo9u1sG7BSpAFgTk6ZtINzSxgf82rGY_1qdpxwN0s4ot5WXuQM4MW84QO--zTzXThFES58isd0k5SgpxhNnlI7QZHQK51yzU5X0cXdNmo6_TvfX8szoOqMSL0ch0vef73N4IwTVYtzE5fucqSUe_-H5HSq983nfXeuaHKvlYqDDUOKUhrmd5RYK71sdwctIpKpjAh1QCXCce2fk6ZfdGwaEvdp1X35lNPXmVrMoYZFWoGgVwHSoafnmY7o4KRjwNsvhEnGNOES4fhotLyxw&ici=nav_bar&icn=user_register&loc_dest=compare%20colleges
Best of luck.