Identifying high-performance, system-level microgrid designs is a significant challenge due to the overwhelming array of possible configurations. Uncertainty relating to loads, utility outages, renewable generation, and fossil generator reliability further complicates this design problem. In this paper, the performance of a candidate microgrid design is assessed by running a discrete event simulation that includes extended, unplanned utility outages during which microgrid performance statistics are computed. Uncertainty is addressed by simulating long operating times and computing average performance over many stochastic outage scenarios. Classifier-guided sampling, a Bayesian classifier-based optimization algorithm for computationally expensive design problems, is used to search and identify configurations that result in reduced average load not served while not exceeding a predetermined microgrid construction cost. The city of Hoboken, NJ, which sustained a severe outage following Hurricane Sandy in October, 2012, is used as an example of a location in which a well-designed microgrid could be of great benefit during an extended, unplanned utility outage. The optimization results illuminate design trends and provide insights into the traits of high-performance configurations.