Both courses are good and are in demand. The opportunities and faster growth are not so much within the type of degree, as it is within the individual who has the degree. Opportunities are always there. It is up to you to take advantage of them through creative and critical thinking, assertiveness, perseverance, commitment, positive attitude, and the ability to think through long-term benefits. Best is subjective term. What is best for me can not be best for you or vice-versa. Identify your actual interests, aptitudes, strengths, and weaknesses and match it with the choices you have to shortlist the apt one for you.
Best colleges to pursue Microbiology are:
Lovely Professional University
Bharath University, Chennai
Devi Ahilya Vishwavidyalaya
Jiwaji University, Faculty of Sciences & Faculty of Life Sciences
Delhi University
Christian Medical College, Vellore
You can do biotechnology related courses from:
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 
Aligarh Muslim University of Mumbai
VIT, BITS.

Biotechnology is a highly interdisciplinary field that combines biological sciences with engineering technologies to manipulate living organisms and biological systems to produce products that advances healthcare, medicine, agriculture, food, pharmaceuticals and environment control. After B.Sc biotechnology the job options like pharmaceutical companies, chemical companies, bio-processing industries, agriculture related industries, diagnostic laboratories and hospitals.

With a degree of M.Sc  in microbiology, you can get opportunities in various fields like healthcare organizations, forensic science laboratories, environmental organizations, higher education institutions, food and drink, publicly funded research organizations, pharmaceuticals etc.

The colleges for M.Sc Biotechnology:

Dr. B. Lal Institute of Biotechnology, Jaipur

Institute of Applied Sciences and Humanities, GLA University, Mathura

Amity University, Jaipur 

The colleges for M.Sc Microbiology you can prefer given below:

Amity University
Bharath University, Chennai
Devi Ahilya Vishwavidyalaya
Jiwaji University, Faculty of Sciences & Faculty of Life Sciences

Good Luck!