In this paper, we present a full 3-D real-space quantum-transport simulator based on the Green's function formalism developed to study nonperturbative effects in ballistic nanotransistors. The nonequilibrium Green function (NEGF) equations in the effective mass approximation are discretized using the control-volume approach and solved self-consistently with the Poisson equation in order to obtain the electron and current densities. An efficient recursive algorithm is used in order to avoid the computation of the full Green function matrix. This algorithm, and the parallelization scheme used for the energy cycle, allow us to compute very efficiently the current-voltage characteristic without the simplifying assumptions often used in other quantum-transport simulations. We have applied our simulator to study the effect of surface roughness and stray charge on the ID-VG characteristic of a 6-nm Si-nanowire transistor. The results highlight the distinctly 3-D character of the electron transport, which cannot be accurately captured by using 1-D and 2-D NEGF simulations, or 3-D mode-space approximations.