Despite the ubiquity of applications of heat transport across nanoscale interfaces, including integrated circuits, thermoelectrics, and nanotheranostics, an accurate description of phonon transport in these systems remains elusive. Here we present a theoretical and computational framework to describe phonon transport with position, momentum and scattering event resolution. We apply this framework to a single material spherical nanoparticle for which the multidimensional resolution offers insight into the physical origin of phonon thermalization, and length-scale dependent anisotropy of steady-state phonon distributions. We extend the formalism to handle interfaces explicitly and investigate the specific case of semi-coherent materials interfaces by computing the coupling between phonons and interfacial strain resulting from aperiodic array of misfit dislocations. Our framework quantitatively describes the thermal interface resistance within the technologically relevant Si-Ge heterostructures. In future, this formalism could provide new insight into coherent and driven phonon effects in nanoscale materials increasingly accessible via ultrafast, THz and near-field spectroscopies.