The complexity of her relationship with each of the time periods is hard to overstate. Her life in the 1970s obviously is much better because she is a free woman with a relatively good and happy life, as well as a caring husband. However, when she is thrust through time and space into the 1800s, she becomes a slave. This would make it easy to assume that she feels much more at home in the present, but it neglects the connections she makes in the past.
In the 1800s, in spite of being a slave, she grows close to Alice, her ancestor, and learns to love several people in that time period. Because of the kinship she feels, she is not quite as alone in the past as one might imagine. Therefore, she feels "at home" in different ways in each time and place. However, in the end, she is more pleased to return to her own time, signifying that she is most at home in her own time period.
If push came to shove, then of course Dana would prefer to remain in 1976, where (though she is still a member of an ethnic minority routinely subjected to racism) she still has her freedom. But the whole point of the story is to show us that such simple binary choices often don't come up in our lives. The present day, like the past that precedes it, is a good deal more complex than we might like to think.
Dana's direct experience of the horrors of slavery has made her understand this, giving her a new perspective on the nature of racial relations. More crucially, it gives her food for thought concerning the complex, multi-faceted nature of American history behind the flag-waving celebrations of the Bicentennial.
Strictly speaking, she's not "at home" anywhere; and perhaps she never will be. But at least now she has a unique perspective on things that allow her to transcend her present condition and see how the past feeds into the present, which in turn can give rise to a more hopeful future: a future free from discrimination and exploitation.
Because Dana is a free woman in 1976 California and a slave on the Weylin plantation in the 1800s, we might assume that she is more "at home" in her modern life and time. However, the novel indicates that Dana's relationship to each of her "homes" is more complicated than that and becomes increasingly so as the novel progresses.
When Dana is first mysteriously plunged back in time and across space, she is obviously frightened and disoriented. As a black woman in the 1800s South, she is automatically considered a slave, despite the fact that in her current life, she is a writer. She is shocked by the racism and the violence of plantation life, and that reality becomes even harsher when she must face it repeatedly.
However, as she goes back and forth from past to present, she learns to survive on the plantation and bonds with the other slaves, especially Alice, who turns out to be one of her ancestors (along with the master, Rufus Weylin). Because she is connected to some of the people on the plantation (through her family line) and forms relationships with her peers, the plantation becomes an odd sort of home for her. Also, because of the abusive interracial relationship between Alice and Rufus, Dana reflects on her own marriage to a white man, Kevin. Although she is happy to return home to her life with Kevin and her freedom, she is forever changed by her experience in the past, and knowing what she now knows about her history, she cannot be truly comfortable in the present either.