Hello,
Both the colleges have got great features. With great faculty and facilities. They are considered first to recruit students from both the states. If you are able to get a seat in either of the two, it will definitely be great. Few students prefer AU to JNTUH because it is much older university, but in my opinion, it doesn't matter much. JNTUH is old too. The facilities are good enough in both the colleges to pursue a masters degree. It is upto you to make a decision here.
Good Luck!