The Congressional Budget Office has issued Taxing the Untaxed Business Sector (23 pages).  From the Preface:

Unlike the income of privately owned for-profit companies, income earned by nonprofit organizations, cooperatives, and business enterprises run by state or local governments is generally not subject to federal income taxes—either at the corporate or at the individual level. Critics argue that such differential tax treatment gives those untaxed entities, which frequently resemble private businesses, an unfair advantage over their for-profit competitors. This Congressional Budget Office (CBO) paper describes the entities that make up the untaxed business sector and examines the potential effects on federal revenue and the U.S. economy from taxing their income. It expands on the analysis that CBO presented in testimony before the House Ways and Means Committee on April 20, 2005.