Boston hospitals cut their energy use by 6 percent over the last three years, saving about $12 million, even as they increased their footprints, according to a new report. The findings come from the Boston Green Ribbon Commission, a group of business and civic leaders that promotes the reduction of greenhouse gas emissions. Paul Lipke, co-coordinator of the commission’s health care group, said hospitals are making progress toward a goal of cutting emissions 25 percent by 2020. Hospitals have taken many steps to reduce energy use, he said, such as installing new lighting and energy-efficient equipment. The report did not specify how individual hospitals performed, saying only that Massachusetts General Hospital, Brigham and Women’s Hospital, and Boston Medical Center are leaders in cutting emissions.