The old covered wagons were called "prairie schooners" because their big canvas tops made them resemble the sailing ships called "schooners." According to the Wikipedia article on Schooners:

A popular legend holds that the first schooner was built by builder Andrew Robinson and launched in Gloucester, Massachusetts where a spectator exclaimed "Oh how she scoons", scoon being similar to scone,[6] a Scots word meaning to skip along the surface of the water.[7][8] Robinson replied, "A schooner let her be."[9]

According to the Wikipedia article, schooners were fast vessels popular in trades that required speed, such as slaving, privateering, and blockade running. The article contains many pictures of various types of schooners.

Wikipedia also contains an article on prairie schooners/covered wagons with some illustrations which show how these vehicles might be thought to resemble oceangoing schooners. 

"Under the Lion's Paw" by Hamlin Garland is set in the prairies of the Midwest at a time when homesteaders and farmers had to settle and improve the land just to claim it. Making a living was hard, but people were willing to work hard because, frankly, they would have starved if they did not do it.

The troubles these homesteaders had were many, and most of them were forces of nature, such as weather and grasshoppers. Sometimes, though, people were the cause of the trouble, as in this story. Tim Haskins and his family are cheated by an unscrupulous landowner and speculator, Jim Butler. But when they first meet Butler, they do not know what he is going to do to them. The Councils are the people whi introduce the Haskins to Butler.

At the beginning of the story, Haskins and his family are on the move because their land and crops were decimated by grasshoppers. They are sick, cold, weary, hungry, and almost defeated when they pull up to the farm owned by the Councils. They have tried to find a place to stay for the night at every house for miles, and they feel as if this home is their last hope. Stephen Council and his wife gladly take them in, and this is where the word "schooner" is used. 

And soon his steaming, weary team, with drooping heads and swinging single-trees, moved past the well to the block beside the path. Council stood at the side of the "schooner" and helped the children out two little half-sleeping children and then a small woman with a babe in her arms.

The Haskins have been traveling in a covered wagon, and Council helps unload all of the family members. 

A covered wagon was often nicknamed a "prairie schooner," and that is the schooner to which the author refers in this story. It is a carriage on wheels that looks like a box below and is pulled by horses. It is covered by a large canvas top, allowing room for people and goods to travel inside and out of the elements.