In this paper, we develop a modeling and optimization procedure for minimizing the operating costs of a combined cooling, heating, and power (CCHP) plant at the University of California, Irvine, which uses co-generation and Thermal Energy Storage (TES) capabilities. Co-generation allows the production of thermal energy along with electricity, by recovering heat from the generators in a power plant. TES provides the ability to reshape the cooling demands during the course of a day, in refrigeration and air-conditioning plants. Therefore, both cogeneration and TES provide a potential to improve the efficiency and economy of energy conversion. The proposed modeling and optimization approach aims to design a supervisory control strategy to effectively utilize this potential, and involves analysis over multiple physical domains which the CCHP system spans, such as thermal, mechanical, chemical and electrical. Advantages of the proposed methodology are demonstrated using simulation case studies.