Colloidal systems consisting of monodomain superparamagnetic nanoparticles have been used in biomedical applications, such as the hyperthermia treatment for cancer. In this type of colloid, called a nanofluid, the nanoparticles tend to agglomeration. It has been shown experimentally that the nanoparticle coating plays an important role in the nanoparticle dispersion stability and biocompatibility. However, theoretical studies in this field are lacking. In addition, the ways in which the nanoparticle coating influences the magnetic properties of the nanoparticles are not yet understood. In order to fill in this gap, this study presents a numerical simulation model that elucidates how the nanoparticle coating affects the nanoparticle agglomeration tendency as well as the effective magnetic relaxation time of the system. To simulate the self-organization of the colloidal nanoparticles, a stochastic Langevin dynamics method was applied based on the effective Verlet-type algorithm. The Néel magnetic relaxation time was obtained via the Coffey method in an oblique magnetic field, adapted to the local magnetic field on a nanoparticle.