Hello Prabhaat, 

Manav Rachna is definitely the better university even though it costs more and has lesser seats. Also as far as I know, Nirma University doesn't have Aeronautical Engineering under its B.tech courses,  so there is no comparison to be made there. 

You can check out top colleges for aeronautical engineering here :  https://engineering.careers360.com/colleges/list-of-aeronautical-engineering-colleges-in-india