The sense of the word is lament for the aborigines.
It is an Iroquois term; and has been used for a personal name.

A song, a poem of itself—the word itself a dirge,
Amid the wilds, the rocks, the storm and wintry night,
To me such misty, strange tableaux the syllables calling up;
Yonnondio—I see, far in the west or north, a limitless ravine, with
        plains and mountains dark,
I see swarms of stalwart chieftains, medicine-men, and warriors,
As flitting by like clouds of ghosts, they pass and are gone in the 
        twilight,
(Race of the woods, the landscapes free, and the falls!
No picture, poem, statement, passing them to the future:)
Yonnondio! Yonnondio!—unlimn'd they disappear;
To-day gives place, and fades—the cities, farms, factories fade;
A muffled sonorous sound, a wailing word is borne through the air
        for a moment,
Then blank and gone and still, and utterly lost.