In the Traditional Ballad Index, the tune (according to Fuld) was in print in 1899 in "Old Plantation Hymns" but the text was "When the Chariot Comes." Fuld assumed that the lyrics of "She'll be Comin' ..." were more recent. The first printing was in Carl Sandburg, The American Songbag, 1927, pp. 372-373. Sandburg says the old spiritual was "made into "She'll be Comin'...." by mountaineers, and the song spread to railroad work gangs in the midwest in the 1890's."

Here is a piece of the sppiritual for comparison. Note that it is the chariot that is called "she" :

O who will drive the chariot when she comes? (twice)
O who will drive the chariot, O who will drive the chariot,
O who will drive the chariot when she comes?

King Jesus, He'll be driver when she comes, etc.

She'll be loaded with bright angels, etc.

She will neither rock nor totter, etc.

She will run so level and steady, etc.

She will take us to the portals, etc.

Sandburg calls the spiritual "old-time." "When the Chariot Comes" with allusions to the ship as "she," is a remake of "Old Ship of Zion," a spiritual collected in the 1870's.
For comparison, here is a verse from "Old Ship of Zion." (T. F. Seward, Negro Spirituals or the Songs of the Jubilee Singers, p. 29)

She is loaded down with angels, Hallelujah,
She is loaded down with angels, Hallelu,
And King Jesus is the captain,
And he'll carry us all home. Oh glory hallelu.

The "she" of the ship has turned into a chariot into a woman in the song.