Currently, the colloidal systems of monodomain superparamagnetic nanoparticles are used in biomedical applications, such as hyperthermia treatment for cancer. In this type of colloid, called nanofluid, there is a tendency of nanoparticle agglomeration. It has been shown experimentally that the nanoparticle coating plays an important role in the nanoparticle dispersion stability and biocompatibility, which role was theoretically understudied so far. Also, the implications of nanoparticle coating on the magnetic properties of the nanoparticles have been little studied. This paper presents the theoretical study, by numerical simulation, on how the nanoparticle coating affects the tendency of agglomeration of the nanoparticles and the Néel relaxation time – or the effective magnetic relaxation time of the system. For simulating the self-organization of colloidal nanoparticles, we apply a Langevin dynamics stochastic method based on an effective Verlet-type algorithm, and the Néel magnetic relaxation time is assessed through the Coffey method in oblique magnetic field, adapted to the local magnetic field on a nanoparticle.