Msc zoology is a 2 year postgraduate course that encompasses the study of existing  and extinct animals.

Msc botany is a 2 year postgraduate course that aims to deliver deeper knowledge of intricate subject of plant biology.

It totally depends on your interest of you have interest in animal life then go for MSC zoology and if you have interest in plant life then take msc botany.

As per career point of view zoology is better than botany because in post graduation you will learn about many topics like biomedical techniques, cytology, endocrinology, embryology , ornithology,marine science, poultry, fish science and etc. So you have bright future in zoology as compared to botany

I hope this helps you

Good luck