Comprehensive Rail Infrastructure Investment Act of 2009 - Amends the Internal Revenue Code to: (1) allow a tax credit through 2012 for 25% of the cost of new qualified freight rail infrastructure property and qualified locomotive property; (2) allow a taxpayer election through 2012 to expense the acquisition, construction, or erection costs of qualified freight rail infrastructure property; and (3) extend through 2012 the tax credit for qualified railroad track maintenance expenditures and modify requirements applicable to such expenditures.