You can do both courses. You should go for M.Sc Biotechnology, M.Sc Biotechnology will increase the chances of employment and better career growth. You can do it from The University of Hyderabad-School of Life Sciences, University of Mumbai-Institute of Chemical Technology, National Dairy Research Institute 

Rajiv Gandhi Center for Biotechnology 
Lovely Professional University 
Delhi Technological University-Department of Biotechnology, Indian Institute of Technology-Department of Biochemical Engineering & Biotechnology, Delhi University
Banaras Hindu University
Jawaharlal Nehru University 
 University of Mumbai

You should go for Msc In Biotechnology or Go for Masters In Biotechnology from Universities in USA which jave excellent learning methodology for live cases. 

You can also tak eup Integrated Ms+PHd Courses in Biotechnology which is of 5-6year duration depending on each University.

Salary prospects after this is at 75000US Dollars per year on average.