Si nanocrystals, terminated with cyclohexane and allylamine, were analyzed using analytical ultracentrifugation (AUC), dynamic light scattering (DLS) and transmission electron microscopy. We found that AUC yielded equivalent particle size distribution data to other nanoparticle characterization techniques, while also providing important information not probed by techniques such as DLS regarding the relative size of the particle core and shell components and the overall effective particle density. Estimates of particle core and shell dimensions are consistent with the particle's optical properties within the quantum confinement representation and available theoretical Si nanocrystal models. Measurement of sedimentation velocity in several solvents with different densities presents a way to circumvent the ambiguity of simultaneous fitting of particle density and sedimentation coefficient and allows us to significantly reduce the uncertainty in the estimates of particle hydrodynamic diameter by finding the effective particle density value.