Church Publishing's Bookstore—The Episcopal Church's official publishing arm
Cowley Publications—the publishing company run by the Society of St. John the Evangelists, a group of Episcopal monks
Eerdmans—is an independent Christian bookseller with some great titles. They also have Eerdmans Books for Young Readers
The Morehouse Group—the Episcopal arm of the Continuum publishing group
Orbis Books—the publishing arm of the Maryknoll priests within the Roman Catholic Church, they offer some great books including Christianity Rediscovered
If you want one great site for finding all of the above and more, there is ChristianBook.com a megastore with great prices on a wide selection of Christian books.