Is it foolishness if I choose BITS Goa CSE over the top NITs CSE?

Choosing neither of those choices would be outright foolishness. You would be foolish if you waste the chance of getting a seat here. 

BITS Goa and top NITs, both have their merits. Speaking from a friend’s experience with BITS Pilani Goa campus has great opportunities for CSE and for the overall development of students as well.

You can talk to someone from NITs about how things are there to get an idea, and then make a choice. Both institutions produce good engineers, so irrespective of what you choose, it will help you if you use the opportunity and facilities offered properly.