This is a Black American folk song, originating in the slavery era. At that time, it was dangerous for enslaved people to speak openly about their concerns, so many songs of the era have hidden or concealed meanings. As a folk song, however, neither the lyrics nor the interpretations are fixed, so it can be difficult or impossible to make a definitive determination.
Like many of the most popular lullabies and nursery rhymes of many traditions (compare Rock a Bye Baby or Ring Around the Mulberry Bush there's some dark and ominous imagery here. It's perhaps most instructive to compare it to All the Pretty Horses, another lullaby with similar origins, and a more established meaning. As in that song, we can surmise that this song is being sung by an enslaved caretaker of a baby belonging to the slavemasters, leading to a mix of tenderness and anger in the lyrics.
Your momma gone away and your daddy's gone to stay
Didn't leave nobody but the baby
The "momma" having gone away indicates that the woman singing is not the baby's actual mother. Likewise, the baby's father is also out of the home.
Everybodys gone in the cotton and the corn
Didn't leave nobody but the baby
With all the masters gone, the baby is at the mercy of its caretaker.
She's long gone with her red shoes on
Gonna need another loving baby
The mother is out having fun, and doesn't care what happens to her child. She might need a new one, because her current child may not have long to live.
You and me and the devil makes three
Don't need no other loving baby
This moves more into pure speculation, but "don't need no other loving baby" may be a veiled reference to her being unable to take care of her own children (as in All the Pretty Horses) because of being forced to caretake her master's child. The devil is present, because she is having fantasies about killing the baby in revenge.
Come lay your bones on the alabaster stones
And be my ever loving baby
This seems like the most clear threat in the song --the alabaster stones, are, of course, the headstones in the graveyard.
Compare also "Summertime," as discussed here: What's the origin of the phrase "Rise Up Singing"? Although not an authentic slave-era lullaby, "Summertime" draws upon many of the same themes, including the caretaking of someone else's child, and the veiled threat.