Hii there, congratulations to you!!

Dear candidate, hope you are doing well, well the question you asked is very complicated and diverse if you think about your future. But there are some aspects where you must think about.

IIST and new IIT's like IIT PATNA, Hyderabad, etc. can be compared but IIT is more a brand and it provides you much more wide range of opportunities if you get into one.

Being in IIST there are high chances to go into ISRO. The ECE department itself is very reserach oriented and aslo it might provide you job. But you will see yourself revolving around Aerospace.

But in IIT you will get to experience many things, IIT patna is new but it's doing really great in recent years.

IIT colleges have slight high package than IIST. But then you must decide whether you want to opt for ECE or Civil branch. Both are very different. Civil is a preferred choice by boys, but now a days, ECE is also in demand, it is more coding and circuit oriented. There are less opportunities in civil for research but there are few. It is more inclined towards designing and working on  field which you might enjoy.  You can compare both colleges here

https://www.careers360.com/compare-colleges

All the best!