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See the field you mentioned above are somewhat related like either of the subject you take at some place you will have to go throught the other fields subject. Another thing you must know is that if you actually want to make a good career in either of the field you must be prepared to do a PhD after your masters. As these subjects are more of a research oriented fields rather than just doing a masters degree and going for a job. Also in most of the institutes the masters program is not alone enough to give you a good job. You will have to go for a PhD after that. In both of fields the thing you should have in your mind is to get the best institute.
Subject wise you will not find much difference but the thing that will actually help you in these courses is your lab experience. You must try to get admission for your masters course in institutes like IISc, JNU, IITs (for biotechnology through GATE exam), IISER, NCBS etc. these are some of the priemere institutes having courses in this field so whatever core branch in science whether biochemistry, biotech or others like neuroscience (NBRC), microbiology, genetics, pathology etc. you can get in one of those institutes that will best help you in your Msc. If you have a mind set of doing a job after your Msc the most job providing area is microbiology as you can find placements in pathological and diagnostic labs or hospital and also in industry. Other fields mostly requires a PhD and once you do a good PhD you will be best placed. So it is upto you that how much can you study depending on that you will have to take decision. If you are not sure to make your career in science than you can still change your stream to fields like MBA and can get jobs after that.