Operators of Electric Autonomous Mobility-on-Demand (E-AMoD) fleets need to make several real-time decisions such as matching available vehicles to ride requests, rebalancing idle vehicles to areas of high demand, and charging vehicles to ensure sufficient range. While this problem can be posed as a linear program that optimizes flows over a space-charge-time graph, the size of the resulting optimization problem does not allow for real-time implementation in realistic settings. In this work, we present the E-AMoD control problem through the lens of reinforcement learning and propose a graph network-based framework to achieve drastically improved scalability and superior performance over heuristics. Specifically, we adopt a bi-level formulation where we (1) leverage a graph network-based RL agent to specify a desired next state in the space-charge graph, and (2) solve more tractable linear programs to best achieve the desired state while ensuring feasibility. Experiments using real-world data from San Francisco and New York City show that our approach achieves up to 89% of the profits of the theoretically-optimal solution while achieving more than a 100x speedup in computational time. We further highlight promising zero-shot transfer capabilities of our learned policy on tasks such as inter-city generalization and service area expansion, thus showing the utility, scalability, and flexibility of our framework. Finally, our approach outperforms the best domain-specific heuristics with comparable runtimes, with an increase in profits by up to 3.2x.