I always use dotmap for this. Although it does not extend to 3 tile radius, it's easy to mark the extra territory if you click one tile to the left, right, top, and bottom of the city center.
reply to how to use dotmap:
By pressing Alt-X, you can choose a color from the palette on the top left, and mark on the map your future city locations. right click on an existing center mark to erase it, or right click on the map where there isn't a center mark to leave the edit mode. You can also toggle the edit mode off by Alt-X again. The markings are still display, until you press Ctrl-X to toggle it off. They can be showed again by the same key.