Sierra Nevada, maybe? I've no idea how much beer they move in a year, but I bet it's a lot more than you'd think, given how ubiquitous it seems to be, for a craft brewery.
Edit: Maybe Shiner, too?
Sierra's by far the next closest after Boston Beer Co and Yuengling.
The sneaky one is 7th place--Craft Brewer's Alliance owns Red Hook and Widmer and does distribution for Kona and Goose Island.
Top 20 as of a couple years back:
1. Anheuser-Busch InBev St. Louis, MO
2. MillerCoors Brewing Co. Chicago, IL
3. Pabst Brewing Co. Woodridge, IL (Doesn't brew--they contract it out)
4. Boston Beer Co. Boston, MA
5. D. G. Yuengling and Son Inc. Pottsville, PA
6. Sierra Nevada Brewing Co. Chico, CA
7. Craft Brewers Alliance, Inc. Woodinville, WA
8. New Belgium Brewing Co. Fort Collins, CO
9. Genessee Brewing Rochester, NY (Formerly High Falls Brewery; they brew Genessee Cream Ale, J.W. Dundee's Honey Lager and others)
10. Spoetzl Brewery Shiner, TX (Shiner Bock)
11. Pyramid Breweries Inc. Seattle, WA
12. Deschutes Brewery Bend, OR
13. Iron City Brewing Co. Pittsburgh, PA
14. Minhas Craft Brewery Monroe, WI (Huber, Rhinelander, Mountain Crest)
15. Matt Brewing Co. Utica, NY (Saranac)
16. Boulevard Brewing Co. Kansas City, MO
17. Full Sail Brewing Co. Hood River, OR
18. Magic Hat Brewing Co. Burlington, VT
19. Alaskan Brewing Co. Juneau, AK
20. Harpoon Brewery Boston, MA