(Quick and dirty) modification of http://stevegrunwell.com/blog/woocommerce-restrict-shipping/ to help Katie from http://noizepro.com/ with limiting WooCommerce shipping for two shipping methods.

gistfile1.php

<?php

/**
 * Return an array of restricted shipping locations for WooCommerce
 * 
 * Restricted locations include Alaska, American Samoa, Guam, Hawaii, North Mariana Islands, Puerto Rico,
 * US Minor Outlying Islands, and the US Virgin Islands
 * 
 * @return array
 */
function grunwell_get_restricted_shipping_locations() {
  return array( 'AK', 'AS', 'GU', 'HI', 'MP', 'PR', 'UM', 'VI' );
}

class Grunwell_Shipping_Free_Shipping extends WC_Shipping_Free_Shipping {
  /**
   * Limit the availability of this shipping method based on the destination state
   *
   * @param array $package
   * @return bool
   */
  public function is_available( $package ) {
    $restricted = grunwell_get_restricted_shipping_locations();
    if ( in_array( $package['destination']['state'], $restricted ) ) {
      return false;
    }
    return parent::is_available( $package );
  }
}

class Grunwell_Shipping_Flat_Rate extends WC_Shipping_Flat_Rate {
  /**
   * Limit the availability of this shipping method based on the destination state
   *
   * @param array $package
   * @return bool
   */
  public function is_available( $package ) {
    $restricted = grunwell_get_restricted_shipping_locations();
    if ( in_array( $package['destination']['state'], $restricted ) ) {
      return false;
    }
    return parent::is_available( $package );
  }
}
 
/**
 * Make WooCommerce load Grunwell_Shipping_Free_Shipping instead of WC_Shipping_Free_Shipping
 * @param array $classes An array of classes assembled by Woocommerce::core_shipping
 * @return array Our filtered $classes
 */
function grunwell_override_free_shipping_class( $classes ) {
  if ( $key = array_search( 'WC_Shipping_Free_Shipping', $classes ) ) {
    $classes[ $key ] = 'Grunwell_Shipping_Free_Shipping';
  }
  if ( $key = array_search( 'WC_Shipping_Flat_Rate', $classes ) ) {
    $classes[ $key ] = 'Grunwell_Shipping_Flat_Rate';
  }
  return $classes;
}
add_filter( 'woocommerce_shipping_methods', 'grunwell_override_free_shipping_class', 11 );