First reference to Hunky, 1861, in Vanity Fair, story by Ward: "He (Moses) folded her to his hart, with the remark that 'he was a hunkey boy.'" OED
1878, Bret Harte: "Man on Beach" (novel); "She's all hunky, and has an appetite." OED

The first made me think of African-American origins, but I have not seen it in any reminiscences or songs of slavery days, etc. Only the later "Hunky-Dory."
"Hunky-Dory" was a blackface song, 1900. (American Memory, sheet music).
A song sheet from Civil War time, Skedaddle Song, had the line "Dey rebels, dey am hunky boys, quite fond of song and rhyme, sah!" (In American Memory)
"Hunkies" appeared in "Jim crow Complete, 150 verses, but meant sitting on your but, hunkered down, a much older usage and a different word. (American Memory)