In many applications of multi-agent systems (MAS), a set of leader agents acts as control inputs to the remaining follower agents. In this paper, we introduce an analytical approach to selecting leader agents in order to minimize the total mean-square error of the follower agent states from their desired value in steady-state in the presence of noisy communication links. We show that, for a set of link weights based on the second-order noise statistics, the problem of choosing leaders in order to minimize this error can be solved using supermodular optimization techniques, leading to efficient algorithms that are within a provable bound of the optimum. We formulate two leader selection problems within our framework, namely the problem of choosing a fixed number of leaders to minimize the error, as well as the problem of choosing the minimum number of leaders to achieve a tolerated level of error. We study both leader selection criteria for different scenarios, including MAS with static topologies, topologies experiencing random link or node failures, switching topologies, and topologies that vary arbitrarily in time due to node mobility. In addition to providing provable bounds for all of these cases, simulation results demonstrate that our approach outperforms other leader selection methods, such as node degree-based and random selection methods, and provides comparable performance to current state of the art algorithms.