This list is not inclusive but here we are:
Eric Wittenberg's Ironclad Publishing is well worth your time: I particularly enjoyed A Little Short of Boats and intend to buy Dave Smith's Pemberton book next.
Butternut and Blue keeps a low profile but this is a must visit for a copy of Tim Reese's High Water Mark, central to understanding McClellan's intended outcome for the battles in the gaps.
Morningside Bookshop is a book store that publishes a long list of titles. The quality of the paper and bindings exceeds the standards enjoyed in the heyday of publishing. My Baldy Smith bio came from Morningside.
The Camp Pope Bookshop is another retailer/publisher. The books look very well made and focus on regimental level material in the western theater.
Westholme publishes a lot of ACW titles, though it's not exclusively about the Civil War and it's larger than the publishers listed so far. I will be enjoying Stealing the General by Russel S. Bonds during my Christmas vacation.
Savas Beatie is like Westholme in terms of size and focus. We speak much here of Army of the Potomac, but this house publishes important Civil War books consistently. I'm a little bit off topic in my S-B reading currently with Indian War Veterans.
If you can encourage a Civill War publisher this season, why not do so?