Heat generation in miniature electronic devices is a limiting factor that often adversely affects device performance. One prominent remedy for this problem is to adopt nanofluid based microchannel heat sinks embedded with pin fins. The performance of these heat sinks depends on their geometry and coolant properties. Aside from these geometrical aspects, there is a dearth of studies on the effects of nanoparticle properties on heat transfer enhancement. In this study, the effects of nanoparticle properties on heat removal performance are modeled using a nanofluid two-component model. It is shown that the nanoparticle distribution plays important roles in heat transfer, and, unlike homogeneous nanofluid models, the flow patterns in the system follow the nanoparticle distribution. Moreover, it is found that the influence of nanoparticles on heat transfer depends both on the pin size and the flow regime. While there is a monotonic dependency between the nanoparticle effect and the pin size at small Reynolds numbers, this effect is non-monotonic at high Reynolds numbers. Nanofluid viscosity is also shown to have adverse effects on heat transfer improvement, and the effect is more detrimental as the inertial forces increase. The particle size and surface energy are also found to change the whole picture of heat removal process due to particle agglomeration and deposition. Therefore, based on the nanoparticle properties, a characteristic curve is introduced, using which, nanoparticles can safely improve heat transfer.