Doing MS from BITS Pilani with wipro is good or bad?

Well, it depends on your goals and priorities. BITS Pilani MS is a great option if you just want to improve your profile and maintain a good status in society. But if you are taking this program to uplift your career then you will be regretting it big.

My uncle who works for an MNC often is entrusted with the job of hiring freshers from well-Reuter colleges and claims that MS students aren’t given any special attention unless they are from IIT or NIT. 

The MS program offered by WIPRO is a scheme to mislead employees to believe that a useless degree is better than anything. They will use this degree as a lash on you to ensure you stay committed to the company and work at a discounted rate. It's better to not fall for such schemes and look at the bigger picture. Your salary will never increase if you stick to these companies.

So, if you are looking for some certifications, then go for some niche skills that are more valuable than a BITS Masters Degree.