fwiw, Waikoloa Coast Divers is on-site at the Hilton. They keep their boat in A-bay there.
Big Island Hawaii Diving on the Kona Kohala Coast with Waikoloa Divers It's about a 30-40? min. drive down to Honokohau harbor where most of the operators keep their boats.
Besides Mokulele Air there's Go Airlines - they sometimes show up on travel websites as Mesa - their parent company.
go! Airlines - Hawaiian Inter-Island Airline Flights In my experience Hawaiian Airlines was always higher.
If you're trying to keep the costs down on Maui, either stay at one of the cheaper big resorts in Ka'anapali or rent a condo in Kihei. Of course if you go for the whales, that's also high-season so rental rates will be more. Many of the condos in Kihei are across the street from the beach/water so slightly cheaper. We've also found reasonable condos in Napili - it's a short drive from there to most things. My family stayed near Wa'alea once but found they were driving to everything.
There's also the option to shore dive on both islands. From the Hilton more of the dive sites are south of Kona - except a couple of dives near Puako. Place of Refuge is a good one if you want to make the trek. Entries there are often off lava so not the easiest - there's not a lot of beaches near dives in that area. Also dive sites tend to be more spread out - it is the "Big" Island.
Plan on 2-1/2 hours to drive from the Hilton to Volcanoes Nat'l Park. It's not really close to anything. But so worth it if it's erupting.
Hawai'i Volcanoes National Park - Hawai'i Volcanoes National Park It's also at 4000' so don't dive that morning. The only time I wouldn't go to Kona is mid-October - that's Ironman week.
On Maui, more of the shore dives are concentrated in the Kihei/Wailea area. There are some near Ka'anapali and going north from there also. Parking will usually be an issue so get there early. There's also the option for escorted shore diving if that's of interest, Shaka Divers or Maui Dreams Dive Co. in the Kihei area - Tiny Bubbles in the Lahaina area. Extended Horizons also does shore diving. Most entries on Maui are off beaches - a few are a short hike in from the main road.
Scuba Shore Diving Region: Hawaiian Islands shows options for both islands - including site entry pictures.
The Maui Ocean Center is worth a look -
Maui Ocean Center | The Hawaiian Aquarium | Maui Family Activity | (808) 270-7000 - they have a dive in their shark tank also. The helicopter tours are expensive but you get to see a lot of areas practically inaccessible any other way. We flew right up against a waterfall on the NW side of Maui and it's a good way to view Hana without a killer drive. If you golf, either Kapalua or Wailea are worth the price. Especially the Kapalua Bay course. Plan to spend an afternoon looking around Lahaina no matter where you stay. Haleakala is at 10,000' so if you plan to do the bikeride - or see the sunrise - do that on a non-dive day.