The Seebeck coefficient in multilayer graphene is investigated within the density-functional theory, using the semiclassical Boltzmann equations and interpolating the bands in a maximally-localized Wannier functions basis set. We compare various graphene stackings (AA, AB and ABC) both free-standing and deposited on the 4H-SiC(0001) C-terminated substrate. We find that the presence of the SiC substrate can significantly affect the thermopower properties of graphene layers, depending on the stacking, providing a promising way to tailor efficient graphene-based devices.