Navy Secretary Gideon Welles preferred to use distinctively American names for ships. Frigates tended to receive river names, sloops the names of cities or towns (but this schema wasn't all that strictly adhered to). It was also frequent to give the ship a name related to somewhere close to where she was built. As many American place names were native-derived, a lot of those made it into the Navy. Critics of this noted (with some accuracy) that as time went on, only the "polysyllabic and cacophonous" ones were left-- so that the never-completed class of large ocean-going monitors under construction at war's end received the formidable names of Passaconaway, Shackamaxon, Kalamazoo, and Quinsigamond.
Sailors tended to poke a bit of fun at some of these names, too. The monitor Miantonomoh was sometimes referred to as "My-aunt-don't-know-me," for instance, and the river ironclad Chillicothe gained the nickname "Chilly Coffee." (Growing up in Ohio, that one doesn't sound as unusual to me as many of the others, but it's undoubtedly less familiar to others...)