HP Grass Kyorge are pretty rare. It isn't in your average Kyorge moveset. Reliable counters to Kyorge really depend on the set is is using. Specs is hard to counter, but Pokes like Palkia or Latias can take a Water Spout and threathen it out, where Gastrodon and Jynx can take pretty much any hit (expect Thunder for Jynx) it throws at you, part from the random HP Grass' here and there.
Countering Scarf Kyorge is little easier since Ferrothorn and Dialga can take a hit and hit hard back or set ut hazards so that Water Spouts BP drops. Any other type of Kyorge set is stopped by every one of the above named Pokemons.