As you know, there is a difference between the nanoparticle and the nanocrystal. Nanoparticles are in the nano range (usually less than 100 nm) in all external and apparent dimensions. But nano-crystals can also belong to a bulk material which is bounded by the grain boundary.
The size of the nanocrystal is calculated by XRD analysis using scherrer equation and full width at half maximum (FWHM). The calculation of nanoparticle size is possible by TEM, SEM, DLS ... analysis. An analysis does not give a definitive result. You must take XRD and microscope analysis to compare.
Single particle can have multiple crystallites (unless it is single crystal as already mentioned in the previous comment). So, you can't apply Scherrer formula. Moreover FWHM doesn't only depend upon crystallite size you need to consider microstrain too (especially if you synthesise your powder by milling).