You should store the marker object in a var and then unset the map as following:

var markerCluster = new MarkerClusterer(map, markers);

/// ... later on

markerCluster.setMap(null);

after you've done this, you could init a new MarkerClusterer with new markers

Update

since you are using google maps ui plugin here's some additional code. I've added a click even on a button with class reset_markercluster ofcourse this is just to show how to use it to call the map

var _map, _markerCluster;



$(function() {

  $('#map_canvas').gmap().bind('init', function(event, map) { 

    _map = map; // at this point you can call _map whenever you need to call the map



    // build up your markers here ...



    _markerCluster = new MarkerClusterer(_map, markers);  // you could also use map instead of _map here cause it's still present in this function

  });



  $(button.reset_markercluster).click(function(e) {

    e.preventDefault();

    _markerCluster.setMap(null);  // remove's the previous added markerCluster



    // rebuild you markers here ...



    _markerCluster = new MarkerClusterer(_map, newMarkers);



  });

});