sono partito da uno degli esempio online...
codice:
<% 
// qui l'array delle tue latitudini e longitudini
  String[] LatLng = new String[]{"59.329383, 18.06947","59.325383, 18.06547"};  
%>
<!DOCTYPE html>
<html>
  <head>
    <meta charset="utf-8">
    <title>Google Maps JavaScript API v3 Example: Marker Animations</title>
    <link href="https://developers.google.com//maps/documentation/javascript/examples/default.css" rel="stylesheet">
    <script src="https://maps.googleapis.com/maps/api/js?v=3.exp&sensor=false"></script>
    <script>
      var stockholm = new google.maps.LatLng(59.32522, 18.07002);
      var parliament = new google.maps.LatLng(59.327383, 18.06747);
      var marker;
      var map;

      function initialize() {
        var mapOptions = {
          zoom: 13,
          mapTypeId: google.maps.MapTypeId.ROADMAP,
          center: stockholm
        };

        map = new google.maps.Map(document.getElementById('map_canvas'),
                mapOptions);

        marker = new google.maps.Marker({
          map:map,
          draggable:true,          
          position: parliament
        });
<%  
// aggiungiamo i markers via JSP
       for (String s: LatLng)  {
%>
        marker = new google.maps.Marker({
          map:map,
          draggable:true,          
          position: new google.maps.LatLng(<% out.print(s); %>)
        });

<%
       }
%>        
      }
      
    </script>
  </head>
  <body onload="initialize()">
    <div id="map_canvas" style="width: 500px; height: 400px;">map div</div>
  </body>
</html>