Port of Lewiston Development Act of 2004 - Extinguishes for specified deeds located in Nez Perce County, Idaho: (1) the reversionary interests and use restrictions relating to industrial use purposes; (2) the restrictions that no activity be allowed to compete with services and facilities offered by public marinas; and (3) the human habitation or other building structure use restriction in each area in which the elevation is above the standard project flood elevation. Authorizes the use of fill material to raise low areas above the standard project flood elevation for such deeds, except in any low area constituting wetland which requires a permit under the Federal Water Pollution Control Act.