fore-and-aft rigged vessel, originally with only two masts, 1716, perhaps from a New England verb related to Scottish scon "to send over water, to skip stones." Skeat relates this dialectal verb to shunt. Spelling probably influenced by Dutch, but Dutch schoener is a loan-word from English, as are German Schoner, French schooner, Swedish skonert. Said to have originated in Gloucester, Mass., shipyard.
Meaning "tall beer glass" is from 1879, of unknown origin or connection.