Which Format is Faster, Matlab (.mat) or NumPy (.npy)?
From my research:


both can store data in binary format
both store the data type of the data
I am unsure about compression ratios and load time, which seems to be the subtext of your question.


One thing you don't seem to address is what you are loading the data into, or whether you are considering moving from a MATLAB environment to Python environment or visa-versa.

That said, I found this post useful and thought it may be helpful to you if you have not seen it already.  https://stackoverflow.com/a/10997335/3259054 Perhaps you could write a small script to sample some files and see the difference.

Have you considered the HDF5 format?  If you are looking to make a change, you might as well test other options too and HDF5 has a lot of momentum towards becoming the de facto standard for scientific computing.

Finally, purely out of a desire to learn, why are you concerned about the file format if you have memory constraints?