The Great Spirit was the designation given to Mata Nui by the Matoran. A Great Spirit was considered to be extremely powerful, though not at the level of a Great Being.
"Great Spirit" was the name given by the Matoran to the being who controlled their universe. In this sense it was a title, as well as a term of honor. Because of this, when Makuta Teridax controlled the universe, the Matoran did not call him a Great Spirit. After his exile, Mata Nui was not considered a Great Spirit, since he no longer had the powers of one.