Savitribai Phule Pune University is the best option among this for an MSc in Mathematics. Pune University is old and well-reputed. Science faculty of this university is great. You will have more options for your MSc project. SPPU is well known for its research interface.
IIT Mandi and NIT Jaipur offer the advantages of brand value. But these institutes are mostly known for their Applied Science courses.
Savitribai Phule Pune University is a lot better than the other two colleges in the domain of Pure Sciences. The option for an MSc in Mathematics was introduced in IIT Mandi and NIT Jaipur only a few years back. My brother recently graduated from SPPU and his overall experience was extremely good.
It is suggested to go for SPPU over IIT Mandi and NIT Jaipur as the University is a lot better for Pure Sciences.