What you could do is: create a new canvas, then copy/merge the main canvas and the annotations. Finally you can get snapshot of this single canvas.
To get a reference to the canvases...
You can use ReaderControls' getPageContainer method:
$('iframe').contents().find("#pageContainer"+ pageIndex);
Inside the page container are all the canvases and thumbnail images.
Alternative you can get the canvases directly like this:
$('iframe').contents().find("#canvas"+ pageIndex);
$('iframe').contents().find("#annotation"+ pageIndex);
(i.e. the main canvas have ids with its page index like such: canvas0, canvas1, ...
and similary with annotation0, annotation1...)
e.g.
var pc = me.getPageContainer(0);
var canvas = pc.find('#canvas0').get(0);
var annot = pc.find('#annotation0').get(0);
//ctx is canvas context of new canvas
ctx.drawImage(canvas, 0,0);
ctx.drawImage(annot, 0,0);