For proper practice of bansuri notes/swaras which app should be used as reference for Indian/Just/Natural tuning?

What you refer to for practicing the swara on any instrument ( or vocal), is the tanpura. The tanpura gives out many of the swaras of the saptak as part of its harmonics, and is hence the best reference for the natural scale...

While there are many apps available for tanpura, the itablapro app for IOS is quite popular..

There is an app called Carnatic Tuner, which I use to check if my vocal notes are in the correct sur. I believe this is used for tuning the Carnatic flute, but I find it useful as a Hindustani vocal learner, as it provides all scales and a complete set of 12 strutis.