Both IIT BHU CSE and IIT Guwahati MnC are excellent options and the choice of the branch is a personal matter depending on the candidate's preferences rather than the credibility of the branch. Here are a few parameters on which we can draw a general comparison between the two courses.
Both the institutes and branches have their own strengths and weaknesses and the final decision should be based on what you want from your degree. If it’s a competitive environment you are after, go for IIT BHU, while if it’s a rich college life experience you want, then IIT Guwahati is your destination.