How to apply filter to specific datatable

You could create an array of tables to have the filter - then in your filter check if the current table is present in that array ... something like :

// setup an array of the ids of tables that should be allowed
var allowFilter = ['productTable'];

$.fn.dataTableExt.afnFiltering.push(function(oSettings, aData, iDataIndex) {

    // check if current table is part of the allow list
    if ( $.inArray( oSettings.nTable.getAttribute('id'), allowFilter ) == -1 )
    {
       // if not table should be ignored
       return true;
    }
    var checked = $('#instock').is(':checked');
    var qntStock = 1; 
    var stockCol = 3; 

    if (!checked) {
        return true;
    }
    if (checked && aData[stockCol] > qntStock) {
        return true;
    }

    return false;
});

you can do something like this: add a parameter to the configuration:

var oTable = $('#productTable').dataTable({
        "applyFilter":true,
        "aoColumnDefs": [{
            "sClass": "my_class", 
            "aTargets": [4]
            }],
        "bAutoWidth": false,
        "iDisplayLength": 100,
        "fnDrawCallback": function() {
            $("td.my_class").editable(function(value, settings) 
            { 
                return(value);
            }, 
            {
                indicator : 'Save...',
                tooltip   : 'Click to Edit...'
            }
            );
        }
    });

and then, verify if your filter is active:

//Filter Function in Stock 
//$('#productTable').
$.fn.dataTableExt.afnFiltering.push(function(oSettings, aData, iDataIndex) {
    if(oSettings.applyFilter)
    {
        var checked = $('#instock').is(':checked');
        var qntStock = 1; 
        var stockCol = 3; 

        if (!checked) {
            return true;
        }
        if (checked && aData[stockCol] > qntStock) {
            return true;
        }

        return false;
    }
    else
        return true;
 });