So for 一本、we know that 本 is a measure word for long cylindrical objects in class. If you were to order a glass of sake, you would use （お酒の名前）一本ください。My question is when can you use 一杯 for sake?
In alcohol contexts, 本 is the counter for bottles and とっくり (sake bottles), which are usually cylindrical. If the restaurant serves sake poured in a tokkuri along with an ochoko, you can order saying 1本ください. In an izakaya that serves sake in a glass or a cup, you should use 1杯. In both cases, saying ひとつ is always okay, too.
The same goes for ordering beer or wine; 1本 refers to a whole bottle, 1杯 refers to a glass.