We investigate theoretically the effects of surface states over the magnetoresistance of Ni-based organic spin-valves. In particular we perform {\it ab initio} electronic transport calculations for a benzene-thiolate molecule chemically attached to a Ni [001] surface and contacted either by Te to another Ni [001] surface, or terminated by a thiol group and probed by a Ni STM tip. In the case of S- and Te-bonded molecules we find a large asymmetry in the spin-currents as a function of the bias, although the I-V is rather symmetric. This leads to a smooth although not monotonic dependence of the magnetoresistance over the bias. In contrast, in the case of a STM-type geometry we demonstrate that the spin-current and the magnetoresistance can be drastically changed with bias. This is the result of a resonance between a spin-polarized surface state of the substrate and the d-shell band-edge of the tip.