Ok, let me preface this question with the fact that I have created a lot of google maps, but they have been strictly markers and polylines denoting routes and a couple with
It can be done, but will require a rewrite of the MarkerClusterer (probably will simplify it).
You will need to determine how you are going to represent and load the cluster boundary polygons (KML, GeoJSON, native Google Maps API v3 polygons) and probably use the google.maps.geometry.poly.containsLocation(point:LatLng, polygon:Polygon) instead of LatLngBounds.contains to determine which cluster "owns" a marker.