I have heard that it was hard cider but I can't seem to find anything that supports that claim.
Just read through the history section of Clay Risen's American Whiskey, Bourbon and Rye and he seems to indicate that industrialization of whiskey production happened around 1830, and by that point it started to gain favor. Some time before that applejack was quite popular, which is essentially freeze distilled hard cider - not sure if it was the most popular. People also had a taste for imported alcohol; particularly brandy and fortified wines.
A few additional notes from the book that paint a rough picture for the American whiskey industry during the war:
To help pay for the Civil War a whiskey excise tax was passed. This tax pops up a lot in history having been repealed in 1802, passed again in 1813 and repealed once more in 1817. I can only speculate, but this likely had an effect on people's drinking habits.
The whiskey tax passed by Abraham Lincoln rose incrementally from 20 cents per proof gallon to 60 cents, and again to a dollar 50, and finally hit two dollars in 1865. The price rose additionally because grain was used to feed troops and farmers went off to war.
In 1860 kentucky whiskey sold for 25 cents a gallon. It sold for 35 dollars in 1863.
Chuck Cowdery and Mike Veach are two very popular writers on the subject of American whiskey history and they both seem to stress how little data exists from this time.
They also stress the importance of not buying into the history that you might see on the side of a bottle, as a lot of it is purely tall tales passed down through families with no verification available, and at times proof that counter claims.
I recommend either of them to get a better idea of the history of American spirits - but need to reiterate that there are not a lot of easy answers out there.