The origins of the word 'Schooner' meaning a tall glass for beer etc is unknown. The word dates back at least as far as 1879.

The other meaning of 'Schooner' - a two masted fast sailing boat, is also obscure.

[…] perhaps from a New England verb related to Scottish scon "to send over water, to skip stones."

See : Etymonline

Note: The Online Etymology Dictionary maintains a free-access list of the origins of thousands of English words, a significant proportion of which are unknown