Here we present a theoretical analysis of the effect of inelastic electron scattering on spin-dependent transport characteristics (conductance, current-voltage dependence, magnetoresistance, shot noise spectrum, Fano factor) for magnetic nanojunction. Such device is composed of molecular quantum dot (with discrete energy levels) connected to ferromagnetic electrodes (treated within the wide-band approximation), where molecular vibrations are modeled as dispersionless phonons. Non-perturbative computational scheme, used in this work, is based on the Green's function theory within the framework of mapping technique (GFT-MT) which transforms the many-body electron-phonon interaction problem into a single-electron multi-channel scattering problem. The consequence of the localized electron-phonon coupling is polaron formation. It is shown that polaron shift and additional peaks in the transmission function completely change the shape of considered transport characteristics.