It is not appropriate to say whether Botany is better or Zoology. Both of the subjects can lead you to a good career. You should determine on the basis of your interest level. Are you interested more in Zoology than in Botany or is it the other way round?

But in general, studying an M. Sc. in Zoology may open up more number of career options than an M. Sc. in Botany. If you study Zoology, you can pursue a career in Zoology, Animal Biology, Biotechnology, Molecular Biology, Marine Science, Oceanography, Biomedical sciences, Fishery Science, Biochemistry, Microbiology, Genetics, Medical Technology and other related areas. Whereas, studying Botany may somewhat limit your career options. After M. Sc. in Botany, you may have an option in Botany, Agricultural Science, Horticulture, Biotechnology, Molecular Biology, Forestry and other related areas.

Any course in Biotechnology generally leads you to an academic career (research and/ or teaching). And naturally, an M. Sc. in not enough if want to have a very prospective career. You must do a Ph. D. But well, after M. Sc., you can get a chance to work in a research organization like Zoological Survey of India, Botanical Survey of India, Tata Institute of Fundamental Research, Institute of Microbial Technology, National Centre for Biological Science and Indian Institute of Chemical Biology. You can also get a job as a lecturer in a college or University department if you qualify in CSIR-UGC NET or equivalent examination.