I have one LQS that doesn't sell any fabric pattern older than the 80's so there are some place out there that don't have Civil War, Shirtings and 30's fabrics. Google online and you will find lots. Here are a few that I have bookmarked just for Civil War Fabrics.
http://www.bonniebluequilts.com/default.aspx
http://www.reproductionfabrics.com/
http://www.trinityquilts.com/content.php?content_id=1
http://www.bearpawquilting.com/
http://www.shopvintageandvogue.com/
http://www.crafttownfabrics.com/