Biocompatible, hydrophobic nanoparticles show great promise as biomaterials. This paper reports the synthesis, magnetic separation, and characterization of magnetite nanoparticles with polydimethylsiloxane (PDMS) adsorbed onto their surfaces. The particle size distributions were narrowed by employing a magnetic separation/fractionation technique to remove larger particles and aggregates from an original distribution. A probability averaging method that incorporates particle size distributions of the magnetite cores derived from TEM is proposed, together with implementation of a polymer brush model for calculating the thickness of the polymer surfactant, for predicting the sizes and size distributions of these complexes in suspension. The intensity, volume, and number average size distributions in solution were predicted, and the values were compared to sizes of the complexes measured by DLS. This approach provides a tool for a more precise characterization of the size distributions of polymer-nanoparticle complexes relative to previous methods that utilized only a mean (single) core particle size. The predicted sizes of the complexes in dispersion closely approximate measured values from DLS for particles with narrow size distributions. Agreement between the predicted and measured sizes improves as the particle size distribution becomes narrower.