Officials from three states and the District of Columbia signed a new Chesapeake Bay agreement in a ceremony at the downtown waterfront in Baltimore, Md. Lee M. Thomas, Environmental Protection Agency administrator, pledged the Reagan Administration's continued financial support of an intergovernmental effort launched in 1983 to clean up the bay. Similar pledges came from Govs. Gerald L. Baliles of Virginia, William Donald Schaefer of Maryland and Robert P. Casey of Pennsylvania, and Mayor Marion Barry of Washington. The 12-page document was signed by the four elected officials and Kenneth Cole, a Pennsylvania legislator who heads the Chesapeake Bay Commission. The agreement contains deadlines for implementing goals that are intended to improve water quality, regulate growth along the bay and rebuild stocks of fish and oysters.