See both colleges top college in their category. Both branch is also good in their own. You can't differentiate between them just by some facts. 

It should be completely dependent on your choice and what you like. If you like analog electronics and digital , then VLSI is best for you. But if you like and you have good knowledge in electromagnetic theory and antenna communication then RF microwave is best for you. 

Placement wise both college are same. But being IIT IITK attracts more companies. 

But it is completely upto you. Where should you go. If you have no choice at all, then go for IIT KANPUR.

Thank you.