Since all drawing is done in a view's drawRect:
you can only optimize your chart's drawing so it can be made to update only a part of it and use setNeedsDisplayInRect:
(passing the area where the marker should be).
Or you create another UIView subclass that is layered atop of your chart and that does nothing but drawing the markers on a transparent background. Probably easier and faster to implement. It also would have another benefit:
If you make that view only as big as the bounding box of the marker you could also easily animate it, like fading it in and out. Or letting it rotate a little (to see the effect I have in mind, select the "Help" menu in Mac OS X, type something in the search field like "a", and see the marker next to a menu item move a little around a spot).