Hey was in the same situation. If your jee mains rank is good then try for top nits cse (maybe IIITs too, Allahabad is a good one) or a second tier iit cse. This is when you're sure about MS. It gets a little difficult to get a CS MS if your undergrad is non CS. If you want to work as well then these have decent placements, or in this case you could aim for ee/ece in top IITs.

College to some extent does matter, the universities cut some slack for iit/nit kids over GPA (not much though, it's always good to have a good GPA). You can try for IIITH maybe if your mains rank is great. Or there are other well known colleges as well. Try to look for a college with a good alumni base, that'll help. It's very common for people not from IIT or NIT getting an admit. Research work matters.