Which course is best BAMS Or BSC Microbiology?

It depends on your interest both are the good option & has value in its field. But BAMS is good option to opt it has wide scope after this you can go for

Private clinic or General Ayurvedic Practice
Specialized Clinic or Specialized Practice
Government Jobs as Ayurvedic Medical Officer
Research Worker
Healthcare Administration
Health Supervisor

BAMS is a good option in its own ways.
Biotech is still developing in India. There has been new developments and modern techniques which enable to improve quality of the products used in biotechnology whereas BAMS is settled in India.
The scope is:

Private clinic or General Ayurvedic Practice
Specialized Clinic or Specialized Practice
Government Jobs as Ayurvedic Medical Officer
Research Worker
Healthcare Administration
Health Supervisor
Manager in ayurvedic pharmacies

Let me know incase you have any other doubt in this.
Good luck.