We perform molecular dynamics simulations on a bead-spring model of pure polymer grafted nanoparticles (PGNs) and of a blend of PGNs with a polymer melt to investigate the correlation between PGN design parameters (such as particle core concentration, polymer grafting density, and polymer length) and properties, such as microstructure, particle mobility, and viscous response. Constant strain-rate simulations were carried out to calculate viscosities and a constant-stress ensemble was used to calculate yield stresses. The PGN systems are found to have less structural order, lower viscosity, and faster diffusivity with increasing length of the grafted chains for a given core concentration or grafting density. Decreasing grafting density causes depletion effects associated with the chains leading to close contacts between some particle cores. All systems were found to shear thin, with the pure PGN systems shear thinning more than the blend; also, the pure systems exhibited a clear yielding behavior that was absent in the blend. Regarding the mechanism of shear thinning at the high shear rates examined, it was found that the shear-induced decrease of Brownian stresses and increase in chain alignment, both correlate with the reduction of viscosity in the system with the latter being more dominant. A coupling between Brownian stresses and chain alignment was also observed wherein the non-equilibrium particle distribution itself promotes chain alignment in the direction of shear.