Both courses are good but Go for B.Tech in Biotechnology. The three-year B.Sc. Course is conducted as any other Science subject and the students can go for the M.Sc. Course and take up research later. The B.Tech. Course is the better option. Selection will be on the basis of the engineering entrance examination and marks obtained in Plus Two or equivalent examinations in Science subjects. Students who pass the qualifying examination with at least 50 per cent marks in mathematics and as much in mathematics, physics, chemistry, and biotechnology, computer Science or biology taken together are eligible to take the entrance examination. A few universities offer a five-year integrated M.Sc. Biotechnology course for Plus Two students in the Science stream. The biotechnology industry is witnessing good growth worldwide. India will have a competitive advantage in the industry since it is knowledge-intensive. A biotechnologist, depending on the area of specialisation, can find jobs in biotechnology or pharmaceutical companies or in chemical, agricultural, and allied industries. Research institutes and laboratories provide good job opportunities for those with M.Tech. And Ph.D. degrees. Teaching is a good option. Study of, and employment in, biotechnology is research-oriented. 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, DTU

B. Tech Biotechnology is better compared to a BSc in Biotechnology.

A B.Tech from a reputed Institute will be helpful for you and you can develop a lot of good contacts through your professors.

After completion of your B. Tech, you can have options to work in different fields in the Biotech industry

1. Sales and management : companies usually come for campus placements to B. Tech colleges to hire graduates for these jobs

2. Scientific writing : A lot of companies and Biotech institutions requires people who have a good grasp of Biotech field and writing skills

3. Research and development : a masters or Phd degree is usually required to get into core research in biotech companies.

But considering all the factors, a B. Tech from a reputed college is a good option. 

Thank you. 

See scope is dependent upon you. If you dont do well, the branch is not to blame. As for the degree, B.Tech is a technical one so value is more for the degree. To get a better idea, you should check major job portals so you have an idea and you also know what kind of jobs are available.