What should I prefer, KJ Somaiya IT or CS from Thadomal Shahani?

There isn't much of a difference between IT and CS, forget institutes individually where you would pursue them. Both CS and IT happen to consist of more or less the same subjects and the course pattern is also similar. There are only a handful of subjects that do not match when it comes to the subject courses of CS and IT and trust me, that isn't as important as it seems. 

Eventually, it is all about your choice of college. It is assumed that you have done some prior research beforehand on the institutes. A former student of this institute who I know would also suggest not giving too much importance to the branches either. 

Also, special mention to KJ Somaiya as along with the benefits of autonomy, you would be able to grab better placement opportunities for yourself at reputed companies with a handsome salary package. The top recruiters of the students of KJ Somaiya are Cognizant, PwC, Amazon, etc. Till now, 90% of students have been placed and the CTC was as high as 29.75 LPA and the average CTC stood at 9.4 LPA. Banking, Financial Services, IT are the sectors which recruited the most students.