If your rank is more than 1000, you’ll probably not get CS/ EE in any good IIT. But if you still wish for an IIT tag, I would recommend you go for a more relaxed branch. This means, picking the branch with the lowest closing rank. I am saying this because apart from the CS/EE/Mathematics group, all the branches come under the category of “others”. Unfortunately, all these “other” branches are equally placed.
If you are passionate about a field, be it Mechanical or Chemical, definitely go for it. With a passion for your field, you will secure a good core job or can even plan your Phd. in that domain. I would also recommend you check the integrated MSc. courses in Mathematics/Statistics/Physics. They might be a better and more beneficial choice.
As far as NSIT/DCE/NITs are concerned, I would recommend you talk to some seniors from the CSE/EE branch to get a better idea. Otherwise, go for a lower branch in the IITs if you do not get a “top notch” branch at them.