GNIS stands for "Geographic Names Information System".
From the GNIS Home Page:
The Geographic Names Information System (GNIS) is the Federal and national standard for geographic nomenclature. The U.S. Geological Survey developed the GNIS in support of the U.S. Board on Geographic Names as the official repository of domestic geographic names data, the official vehicle for geographic names use by all departments of the Federal Government, and the source for applying geographic names to Federal electronic and printed products. The GNIS contains information about physical and cultural geographic features of all types in the United States, associated areas, and Antarctica, current and historical, but not including roads and highways. The database holds the Federally recognized name of each feature and defines the feature location by state, county, USGS topographic map, and geographic coordinates. Other attributes include names or spellings other than the official name, feature designations, feature classification, historical and descriptive information, and for some categories the geometric boundaries. The database assigns a unique, permanent feature identifier, the Feature ID, as the only standard Federal key for accessing, integrating, or reconciling feature data from multiple data sets. The GNIS collects data from a broad program of partnerships with Federal, State, and local government agencies and other authorized contributors, and provides data to all levels of government, to the public, and to numerous applications through a web query site, web map and feature services, file download services, and customized files upon request.
The GNIS database can be searched to find the location of specific locations mentioned in genealogical records. While the focus of the data base is on current names for features, it is often possible to pick up existing features previously known by another name. GNIS also provides links to various mapping services, including in particular the US National Atlas (a product of the US Government, whose images can be used with minimal restriction), and other services such such as