In my opinion, if you are getting a top NIT, then choosing CSE will be a better decision unless you are interested in any other specific branch. As far as comparing the CSE branch in Warangal and Surathkal, both offer similar opportunities and academic experience.
Given all the similarities, choosing one between these two NITs depends more on your personal choices such as proximity to home and crowd. If you are from the home state of Karnataka choose Surathkal but if you are from the home state of Warangal, choose NIT Warangal.
I would recommend you to go for NIT Warangal as it has better opportunities if you are inclined towards research. The alumni base is huge and there is even an innovation garage where the ideas of students are implemented.