We simulate numerically the full dynamics of Faraday waves in three dimensions for two incompressible and immiscible viscous fluids. The Navier-Stokes equations are solved using a finite-difference projection method coupled with a front-tracking method for the interface between the two fluids. The domain of calculation is periodic in the horizontal directions and bounded in the vertical direction by two rigid horizontal plates. The critical accelerations and wavenumbers, as well as the temporal behaviour at onset are compared with the results of the linear Floquet analysis of Kumar and Tuckerman [J. Fluid Mech. 279, 49-68 (1994)]. The finite amplitude results are compared with the experiments of Kityk et al. [Phys. Rev. E 72, 036209 (2005)]. In particular we reproduce the detailed spatiotemporal spectrum of both square and hexagonal patterns within experimental uncertainty