Electric vehicles (EVs) are being rapidly adopted due to their economic and societal benefits. Autonomous mobility-on-demand (AMoD) systems also embrace this trend. However, the long charging time and high recharging frequency of EVs pose challenges to efficiently managing EV AMoD systems. The complicated dynamic charging and mobility process of EV AMoD systems makes the demand and supply uncertainties significant when designing vehicle balancing algorithms. In this work, we design a data-driven distributionally robust optimization (DRO) approach to balance EVs for both the mobility service and the charging process. The optimization goal is to minimize the worst-case expected cost under both passenger mobility demand uncertainties and EV supply uncertainties. We then propose a novel distributional uncertainty sets construction algorithm that guarantees the produced parameters are contained in desired confidence regions with a given probability. To solve the proposed DRO AMoD EV balancing problem, we derive an equivalent computationally tractable convex optimization problem. Based on real-world EV data of a taxi system, we show that with our solution the average total balancing cost is reduced by 14.49%, and the average mobility fairness and charging fairness are improved by 15.78% and 34.51%, respectively, compared to solutions that do not consider uncertainties.