The interaction of electrons with atomic motion critically influences charge transport properties in molecular conducting junctions and quantum dot systems, and it is responsible for a plethora of transport phenomena. Nevertheless, theoretical tools are still limited to treat simple model junctions in specific parameter regimes. In this work, we put forward a generalized input-output method (GIOM) for studying charge transport in molecular junctions accounting for strong electron-vibration interactions and including electronic and phononic environments. The method radically expands the scope of the input-output theory, which was originally put forward to treat quantum optic problems. Based on the GIOM we derive a Langevin-type equation of motion for molecular operators, which posses a great generality and accuracy, and permits the derivation of a stationary charge current expression involving only two types of transfer rates. Furthermore, we devise the so-called "Polaron Transport in Electronic Resonance" (PoTER) approximation, which allows to feasibly simulate electron dynamics in generic tight-binding models with strong electron-vibration interactions. To illustrate the breadth of applications of the GIOM-PoTER technique, we analyze prototype molecular junction models with primary and secondary vibrational modes. For short chains, the charge current reduces to known limits and reasonably agrees with exact numerical simulations (when available). For extended junctions the current displays a turnover from phonon-assisted to phonon-suppressed transport. Nevertheless, the onset of ohmic behavior requires extensions beyond the PoTER approximation. As an additional application, we consider a cavity-coupled molecule junction. Here we identify a cavity-induced suppression of charge current in the single-site case, and observe signatures of polariton formation in the current-voltage characteristics in the strong light-matter coupling regime. A critical understanding gained from the GIOM-PoTER scheme is that the single-site vibrationally-coupled model is deceptively simpler, and amenable to approximations than multi-site models. Therefore, benchmarking of methods should not be concluded with the single-site case. The work manifests that the input-output framework, which is normally employed in quantum optics, can serve as a powerful and feasible tool in the realm of electron transport junctions.