This seems to be a very old post but sharing as it might help someone else. if you want to search a point geometry within a polygon, you will have to use within filter while doing spatial query on polygon layer.
Code Example:
pt = Point({"x" : -10392706.32194956, "y" : 5622351.110157302, "spatialReference" : {"wkid" : 4326 }}) //constructing point geometry
gf = within(pt,sr=4326) // this is geometry_filter we are creating which will be passed in the query below. you will have to import within filter from arcgis.geometry.filters import within
polygon_features = polygon_layer.query(where='1=1',geometry_filter=gf,out_fields='field1,field2',return_geometry= False) // if you want polygon geometry to be returned then remove return_geometry= False.