Is IIIT Hyderabad really best in MS or M.Tech in CSE?

It's difficult to say if IIIT Hyderabad MTech or MS CSE is the best or not as it's a matter of personal preference. What might be best for you, may not be for someone else. So first, you have to identify your interests and goals. Usually, IIIT Hyderabad is suitable for 

• People who want to pursue high-level research in CS
• People who are determined to pursue a career in CS and want to polish their CS skills and fundamentals
• People who are just after the IIIT and CS tag

Every institute has something or the other to offer so comparing them isn't right. Instead, look at the bigger picture and understand what you are looking for in your degree and which institute will serve you best.