Disable Payment Methods for Specific Product Category or Shipping In Woocommerce

add_filter( 'woocommerce_available_payment_gateways', 'greenbackend_unset_gateway_by_category' );
  
function greenbackend_unset_gateway_by_category( $available_gateways ) {
    if ( is_admin() ) return $available_gateways;
    if ( ! is_checkout() ) return $available_gateways;
    $unset = false;
    $category_ids = array( 288, 73,113,69 );
    foreach ( WC()->cart->get_cart_contents() as $key => $values ) {
        $terms = get_the_terms( $values['product_id'], 'product_cat' );    
        foreach ( $terms as $term ) {        
            if ( in_array( $term->term_id, $category_ids ) ) {
                $unset = true;
                break;
            }
        }
    }
    if ( $unset == true ){ 
    	unset( $available_gateways['cheque'] );
    		unset( $available_gateways['cod'] );
    	
    }
    return $available_gateways;
}

You could also disable shipping costs for specific payment method with the following code:

add_action( 'woocommerce_package_rates','show_hide_shipping_methods', 10, 2 );
function show_hide_shipping_methods( $rates, $package ) {
    // HERE Define your targeted shipping method ID
    $payment_method        = 'cod';

    $chosen_payment_method = WC()->session->get('chosen_payment_method');

    if( $payment_method == $chosen_payment_method ){
    	  unset($rates['flat_rate:1']);
        unset($rates['flat_rate:2']);
    }
    return $rates;
}

add_action( 'woocommerce_review_order_before_payment', 'payment_methods_trigger_update_checkout' );
function payment_methods_trigger_update_checkout(){
    // jQuery code
    ?>
    <script type="text/javascript">
        (function($){
            $( 'form.checkout' ).on( 'blur', 'input[name^="payment_method"]', function() {
                setTimeout(function(){
                    $(document.body).trigger('update_checkout');
                }, 250 );
            });
        })(jQuery);
    </script>
    <?php
}

add_action( 'woocommerce_checkout_update_order_review', 'refresh_shipping_methods' );
function refresh_shipping_methods( $post_data ){
    // HERE Define your targeted shipping method ID
    $payment_method = 'cod';
    $bool           = true;

    if ( WC()->session->get('chosen_payment_method') === $payment_method )
        $bool = false;

    // Mandatory to make it work with shipping methods
    foreach ( WC()->cart->get_shipping_packages() as $package_key => $package ){
        WC()->session->set( 'shipping_for_package_' . $package_key, $bool );
    }
    WC()->cart->calculate_shipping();
}