1716, perhaps from a New England verb related to Scottish
scon "to send over water, to skip stones." Skeat relates this dial. verb to
shunt. Spelling probably influenced by Du., but Du.
schoener is a loan-word from English, as are Ger.
Schoner, Fr.
schooner, Swed.
skonert. Said to have originated in Gloucester, Mass., shipyard.
"The rig characteristic of a schooner has been defined as consisting essentially of two gaff sails, the after sail not being smaller than the fore, and a head sail set on a bowsprit." [OED]
Meaning "tall beer glass" is from 1879, of unknown origin.