Recent progress in the field of molecular electronics has revealed the fundamental importance of the coupling between the electronic degrees of freedom and specific vibrational modes. Considering the examples of a molecular dimer and a carbon nanotube double quantum dot, we here theoretically investigate transport through a two-site system that is strongly coupled to a single vibrational mode. Using a quantum master equation approach, we demonstrate that, depending on the relative positions of the two dots, electron-phonon interactions can lead to negative differential conductance and suppression of the current through the system. We also discuss the experimental relevance of the presented results and possible implementations of the studied system.