Hello Aspirant,

Top colleges for MPT are mentioned below:

• Christian Medical University, Vellore
  
• Sri Ramachandra Institute of Higher Education and Research, Chennai 
• Ramaiah Medical College, Bangalore 
• Baba Farid University of Health Sciences, Faridkot
• Manipal University, Manipal
• Maharashtra University of Health Sciences, Nashik

Hii aspirant..

The best colleges in India for pursuing Masters in Physiotherapy are -

• Maharastra University of Health and Sciences, Nashik
• Manipal University, Manipal
• Baba Farid University of Health Sciences (BFUHS), Punjab
• M.S.Ramaih Medical College, Bangalore
• Sri Ramachandra University, Chennai
• Christian Medical College, Vellore
• Pravara Institute Of Medical Sciences University, Ahmed Nagar
• NIMS University, Jaipur
• Hamdard Institute of Medical Sciences and Research ( HIMSR), Delhi
• Janardan Rai Nagar Rajasthan Vidyapeeth, Udaipur
• Maharastra University of Health and Sciences, Nashik

Hope it helps. 

Best of luck.