Cleaner Trucks for America Act of 2009 - Amends the Internal Revenue Code to: (1) increase the credit amount for new qualified alternative fuel motor vehicles with gross vehicle weight ratings of more than 26,000 pounds from $40,000 to $80,000 and allow the transferability of such credit; (2) allow an increased tax credit for alternative fuel vehicle refueling properties that dispense compressed natural gas, liquefied natural gas, or liquefied petroleum gas; and (3) allow such credit amounts against the regular and alternative minimum tax.