"thick fish soup," 1751, American English, apparently named for the pot it was cooked in: French chaudière "a pot" (12c.), from Late Latin caldaria "cooking pot" (source of Spanish calderon, Italian calderone), from Latin calidarium "hot bath," from calidus "warm, hot" (from PIE root *kele- (1) "warm").
The word and the practice were introduced in Newfoundland by Breton fishermen and spread from there to the Maritimes and New England.
CHOWDER. A favorite dish in New England, made of fish, pork, onions, and biscuit stewed together. Cider and champagne are sometimes added. Pic-nic parties to the sea-shore generally have a dish of chowder, prepared by themselves in some grove near the beach, from fish caught at the same time. [John Russell Bartlett, "Dictionary of Americanisms," 1859]
The modern form of it usually features clams. In New England, usually made with milk; the Manhattan version is made with tomatoes. The derogatory chowderhead (1819) is a corruption of cholter-head (16c.), from jolt-head, which is of unknown origin.