It depends on your interest first that you want to opt for which course. 

If we compare both the courses than MSC food qulaity assurance has limited scope on the other hand food science technology has wider scope 

Depending on one’s qualification and interest, there are many options available to choose from food science and technology. “A person can choose to work in food manufacturing industries as it is a sector which needs persons for work from the basic level to the higher level. Positions like new product developer, production supervisor, production executive and quality controller are easily available,” states Sheetal Khadye, R&D manager, Puratos Food Ingredients India Pvt Ltd. There are also marketing and technical service positions available with ingredient suppliers. With the introduction of new food laws, regulatory positions are now also available.

Good Luck!!