We consider transport through finite quantum systems such as quantum barriers, wells, dots or junctions, coupled to local vibrational modes in the quantal regime. As a generic model we study the Holstein-Hubbard Hamiltonian with site-dependent potentials and interactions. Depending on the barrier height to electron-phonon coupling strength ratio and the phonon frequency we find distinct opposed behaviors: Vibration-mediated tunneling or intrinsic localization of (bi)polarons. These regimes are strongly manifested in the density correlations, mobility, and optical response calculated by exact numerical techniques.