(ArcGIS API for JavaScript) Two samples of how to get the points within a certain polygon

geometryEngineSample.js

// Using geometry engine, you can use the contains method to loop through all the points and see if that point is within a polygon. 
// This requires using a nested for loop, so the more points you have then the slower the program may be. 

require(["esri/map",
         "esri/layers/FeatureLayer",
         "esri/tasks/query",
         "esri/tasks/QueryTask",
         "esri/geometry/geometryEngine",
         "esri/graphic",
         "esri/symbols/SimpleMarkerSymbol",
         "esri/Color",
         "esri/symbols/SimpleLineSymbol",
         "esri/layers/GraphicsLayer",
         "dojo/domReady!"
], function (Map, FeatureLayer, Query, QueryTask, geometryEngine, Graphic, SimpleMarkerSymbol, Color, SimpleLineSymbol, GraphicsLayer) {

    //Initializing the map constructor
    var map = new Map("map", {
        center: [-118, 34.5],
        zoom: 8,
        basemap: "topo"
    });
  
    var query = new Query();
    query.where = "1=1"
    query.returnGeometry = true;
  
    var arr = [];
    
    // The query task is used to get the geometry in JSON form.
    var queryPoints = new QueryTask(myURL);
    var queryPolygons = new QueryTask(myURL);
    queryPoints.execute(query, (points) => {
      //Get the points in JSON form do another query on the second layer. 
      queryPolygons.execute(query, (polygons) => {
        //Loop through each point and see if that point is inside a polygon
        points.features.forEach((point) => {
          //console.log(point)
          polygons.features.forEach((polygon) => {
            if(geometryEngine.contains(polygon.geometry, point.geometry)){
              arr.push({'point': point.attributes.CITY_FIPS,'polygon': polygon.geometry});         
            }
          });
        });
      });
    });
  
    console.log(arr);
});

SpatialFilterSample.js

// This sample uses the server to find if any points are within a certain polygon. 
// This option only uses one for loop to go through each polygon and then uses a spatial filter as input to the query for the points.
// For this option your points would need to be on the server either through a map service or a feature layer. 

require(["esri/map",
         "esri/layers/FeatureLayer",
         "esri/tasks/query",
         "esri/tasks/QueryTask",
         "esri/geometry/geometryEngine",
         "esri/graphic",
         "esri/symbols/SimpleMarkerSymbol",
         "esri/Color",
         "esri/symbols/SimpleLineSymbol",
         "esri/layers/GraphicsLayer",
         "dojo/domReady!"
], function (Map, FeatureLayer, Query, QueryTask, geometryEngine, Graphic, SimpleMarkerSymbol, Color, SimpleLineSymbol, GraphicsLayer) {

    //Initializing the map constructor
    var map = new Map("map", {
        center: [-118, 34.5],
        zoom: 8,
        basemap: "topo"
    });
  
    var fl1 = new FeatureLayer("myURL");
    var fl2 = new FeatureLayer("myURL");
  
    var arr = [];
  
    var query = new Query();
    query.where = "1=1"
    query.returnGeometry = true; 
 
    var queryPoints = new QueryTask(fl1.url);
    var queryPolygons = new QueryTask(fl2.url);
  
    queryPolygons.execute(query, (polygons) => {
        polygons.features.forEach((polygon) => {
          query.geometry = polygon.geometry;
          queryPoints.execute(query, (points) => {
            arr.push({'polygon': polygon, 'points': points});
          });
        });
    });
  
    console.log(arr);
  
  //map.addLayers([fl2,fl1])
  //map.addLayer(fl2)
});