Northern Appalachian Economic Development Commission Act of 2006 - Establishes the Northern Appalachian Economic Development Commission to provide advisory strategic guidance and coordination and grant assistance in support of economic development, community development, and natural resource conservation in the Northern Appalachian region in the states of Maine, New Hampshire, Vermont, and New York. Authorizes each affected state to designate local development districts to receive such assistance. Requires the Commission to develop an integrated development strategy for the region. Authorizes the Commission to approve grants to states, local development districts, and public and nonprofit entities for economic development projects in the region.