Which is better: M.Tech in CSE from IIT Hyderabad or M.tech in theoretical computer science in IIT Guwahati?

Assuming that you are research-oriented, I suggest you choose IIT Guwahati MTech in theoretical CS rather than MTech in CSE from IIT Hyderabad. From the choice of your research-related subjects, theoretical CS seems to be the best option. Moreover, the Mathematics and Computer Science department of IIT Guwahati is extremely good with a knowledgeable faculty base.

MTech at IIT Hyderabad on the other hand is more focused on campus-related work rather than actual theoretical knowledge of the subjects. 

It’s important to check if the research interests of the faculty align with your subject interests.