Proposed as a response to the increasing global need for environmental protection, a green port balances economic vibrancy and environmental protection. However, because exhaust emissions (e.g., CO2 or sulfide) are difficult to monitor in and around ports, data on such emissions are often incomplete, which hinders research on this topic. To remedy this problem, this study aimed to formulate a method for collecting CO2 emissions data at their source; this method was applied to collect real-world operating data from a large container-handling company in Taiwan. Specifically, to account for undesirable outputs, we formulated a method that combines (1) data envelopment analysis based on a modified slack-based measure and (2) a multichoice goal programming approach. We found that rubber-tired gantry cranes are the greenest and should be used. Our findings aid port managers in selecting port equipment that best balances between environmental protection and profitability.