Haunter's Attack and Defense aren't going to get much better. Look at that Sp. Atk stat; time to start making use of it
Firstly, go to the Move Relearner, and get Shadow Ball back over Shadow Claw. Level it two more levels for Dark Pulse over Sucker Punch or Mean Look.
Now, what resists both Ghost and Dark? The answer is Steel and Dark. This is easy to take care of; in Goldenrod's Department Store, buy a TM52 Focus Blast, and teach it to Haunter. It might not have the best accuracy, but it will really help against the two types mentioned above.
Onix sucks, to be honest. I'd switch it for a Graveler; it has better stats overall, and learns much better moves by level up, such as Earthquake, Explosion and Stone Edge.
Pidgeot needs a powerful Normal-type move, such as Return (TM27; in Goldenrod, you have to show the happiness lady a very happy Pokémon on Sunday). Replace Gust, which isn't really that good compared to Fly and Wing Attack. It learns Roost in a couple of levels; it might be worth deleting Quick Attack or Wing Attack for it.
Now for Ho-oh. Being a legendary, it's pretty good already. It has a large variety of TM moves you can use on it, if you need some type coverage. For example, Thunder/Thunderbolt will be useful against Water-types, and Earthquake is great against Fire and Rock types. Watch out for Thunder's shaky accuracy (especially if it's sunny); Thunderbolt is difficult to obtain (10000 coins in the Game Corner), and Earthquake is a pain to get again once you've used the one in Victory Road (if you want another one, you'll have to grind 80BP in the Battle Frontier after you beat the Elite Four). Personally, I'd go for Earthquake, to make use of its higher Attack stat. Also worth consideration is Brave Bird, which it learns via the Move Relearner; it's one of the most powerful attacks Ho-oh can learn, but with the downside of taking recoil damage whenever you use it.
As has already been said, Gyarados needs a powerful physical attack. You won't really be needing Whirlpool for much any more (plus it's weak), so that can go. Dragon Rage also gets worse as the opponents' Pokémon get stronger; that can go too. Strength and Dragon Dance are pretty good moves to fill those two slots (level up a bit more for Dragon Dance).
Ampharos, being a pure Electric type, doesn't have a lot of options. Fortunately, it does learn some interesting moves by leveling up; Signal Beam at level 42 and Power Gem at level 59. Signal Beam deals with Grass types; Power Gem isn't that good for type coverage, but can be used for super-effective hits against Bug and Ice types, especially if they happen to resist Electric moves (e.g. Parasect). Like with Haunter, you could try teaching it Focus Blast to help with the Ground types that are also part Rock or Steel.
For leveling up, you could give all your money to your mother in New Bark Town, and repeatedly fight (and possibly lose to) the Elite Four.
You lack Dragon and Ice type moves (Dragon Rage doesn't count), which are useful against the Champion. All his Pokémon are also weak to Rock, though, so Graveler will be very useful. Ho-oh, with its insane stats, will be able to wreck Pokémon a few levels higher than itself.
By the way, you'll want to evolve Haunter and Graveler (assuming you get one); they have to be traded to evolve (a simple trade and trade back will do). If you have Wi-Fi on your DS, you can get help here; if you know anyone IRL that has a Pokémon DS game, even better