Commercial vessels berthed at New York City's marine terminals continuously run fossil fuel-powered auxiliary diesel generators, emitting harmful air pollutants directly into already burdened waterfront communities. Shore power, connecting berthed vessels to the electrical grid and shutting down their auxiliary engines, is an established solution with demonstrated emissions reductions of 80 to 99%, yet no harbor-wide analysis has previously identified priority sites for investment. This study develops a multi-criteria prioritization framework using vessel-level AIS data processed through the MOCEJ emissions model. Six facilities emerge as top priorities: the Manhattan Cruise Terminal, Port Liberty New York, Red Hook Container Terminal, and the Wards Island, Hunts Point, and Newtown Creek wastewater treatment plants. Vessels at these facilities generated 12.8 million kWh of auxiliary energy demand in 2024, emitting 9,855 metric tons of CO₂, 2.45 metric tons of PM2.5, and 0.54 metric tons of SO₂, with over 150,780 residents living within one kilometer of their berths.