Hey,
Both Bachelor of Science in Microbiology and B.Pharma are good at their own places and cannot be compared on any scale. Both are related to different aspects of Science. It entirely depends upon your calling.
Bachelor of Science in Microbiology is a three-year long undergraduate programme and deals with the study of the Biology of bacteria,viruses,protozoa and fungi. The top Institutes are Indian Academy Degree College,Lovely proffesional university etcetera.
B. Pharma is a four-year long undergraduate programme and gives you the degree of a Pharmacists. It includes the study of preparing and conferring drugs and medicines for a number of Illness and deficiencies.
Hope this helps.
Good luck.