Dickinson: While Dickinson does discuss matters of life and death and the soul in many of her poems, her view differs greatly from the American Romantic poets before her. While their poems are filled with praise for God and a desire to perfect the soul in order to please God (See Holmes' "Chambered Nautilus" as an example of this.), Dickinson focuses more on personal experience and human emotions. Her "Heart! We will forget him" and "Because I could not stop for death" demonstrate that Dickinson was interested in the typical human experiences--healing a broken heart and pondering death--but her interest is much more human-centered than "heavenly" focused.
Howells: Howells represents an even more distinct rebellion against traditional religion. His A Modern Instance discusses the breakup of a marriage, which according to traditional Christian beliefs is sacred and a symbol of Christ's relationship with the church. While Howells' predecessors like Henry Wadsworth Longfellow praised the virtues of their spouses and idolized purity of spirit in marriage, Howells strove to portray humans as common folks who struggled with flaws and practical, everyday life.
Twain: Of the three authors mentioned in your question, Twain is arguably the most obvious satirist of traditional religion. Almost all of his novels mock the hypocrisy in Christians from Twain's time period (The Widow Douglass owning slaves even as she is a "good Christian woman" who tries to help civilize Huck; or Huck's struggle to do what his conscience dictates rather than what his "moral," religious society tells him is right--to turn in a runaway slave who will then be sold and separated from his family.)
All three authorswrote after and in response toAmerica's Idealistic Romantic period in which religion was praised, moral virtue upheld, and nature extolled. Their writing as Realists (or in Dickinson's case as one of the founders of New American Poetry) focuses on the gritty reality and practicality of life.