what's the best water type Pokemon in Heart Gold?

Gyrados is an option as well, might as well catch it sinc your forced to battle it. Outside of that, no there isn't many other options, although you can use a Tentacruel, since its actually, despite its commonnesss, quite good.

Lapras could be the one. It could kill grass type pokemon with its ice moves. Their is one strategy with to use perish song, dive, protect, and whirlpool to let it the opponent faint. If you are afraid of grass type attacks, give it a cheri berry to decrease grass type damage. Kingdra is okay, but it does not have a diverse move pool. Their is no good dragon attacks for it also. It is easy to take out and its Fragile. Lapras has the hp to last longer. It is better to use an ice water type to use an ice attack than a water pokemon because lapras will have its ice type STAB boost. It also have water absorb to be immune to water type damage.

Golduck

Feraligatr is pretty powerful, and is my personal favorite (: