Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic simulations partition the environment into subvolumes, track when molecules move between adjacent subvolumes, and are generally more computationally efficient. In this paper, we present the foundation of a multi-scale stochastic simulator from the perspective of molecular communication, for both mesoscopic and hybrid models, where we emphasize simulation accuracy at the receiver and efficiency in regions that are far from the communication link. Our multi-scale models use subvolumes of different sizes, between which we derive the diffusion event transition rate. Simulation results compare the accuracy and efficiency of traditional approaches with that of a regular hybrid method and with those of our proposed multi-scale methods.