Here's how the lyrics appear in Jacobite Minstrelsy (Glasgow: R. Griffin & Co., 1828):

PRINCE CHARLES AND FLORA MACDONALD'S WELCOME TO SKYE.*

There are twa bonny maidens,
And three bonny maidens,
Come over the Minch,
And come over the main,
Wi' the wind for their way,
And the correi for their hame:
Let us welcome them bravely
Unto Skye again.
Come along, come along,
Wi' your boatie and your song,
You twa bonny maidens,
And three bonny maidens;
For the night it is dark,
And the red-coat is gone,
And you're bravely welcome
To Skye again.

There is Flora, my honey,
So dear and so bonny,
And one that is tall,
And comely withal;
Put the one as my king,
And the other as my queen,
They're welcome unto
The Isle of Skye again.
Come along, come along,
Wi' your boatie and your song,
You twa bonny maidens,
And three bonny maidens;
For the lady of Macoulain
She lieth her lane,
And you're bravely welcome
To Skye again.

Her arm it is strong,
And her petticoat is long,
My one bonny maiden,
And twa bonny maidens;
But their bed shall be clean,
On the heather most crain;
And they're welcome unto
The Isle of Skye again.
Come along, come along,
Wi' your boatie and your song,
You one bonny maiden,
And twa bonny maidens.
By the sea-moullit's nest
I will watch o'er the main;
And you're dearly welcome
To Skye again.

There's a wind on the tree,
And a ship on the sea,
My twa bonny maidens,
My three bonny maidens.
On the lea of the rock
Your craddle I shall rock;
And you're welcome unto
The Isle of Skye again.
Come along, come along,
Wi' your boatie and your song,
My twa bonny maidens,
And three bonny maidens:
More sound shall you sleep,
When you rock on the deep;
And you'll aye be welcome
To Skye again.

* The Ettrick Shepherd [Hogg], notwithstanding the childish simplicity or rather absurdity of this reputed translation from the Gaelic, says that there is no song or air he likes better. According to his account too, it was copied verbatim from the mouth of Mrs Betty Cameron of Lochaber, well known for her great store of Jacobite songs, and her attachment to Prince Charles and the chiefs that suffered for him, of whom she never spoke without bursting out a-crying. The Shepherd, reasonably enough, supposes the translation to be Mrs Betty's own composition. [Editor's note.]

[The above lyrics seem to be translated into more conventional Scots spelling from Hogg's version, which can be seen with musical notation in The Jacobite Relics of Scotland.]