Most of the boats leave out of Honokahau (sp) harbor just north of Kailua-Kona. But there's nothing nearby.
So you can either stay at one of the hotels/condos in town or just south of there - there's a lot of properties south along the coast for several miles including some big hotels. We found some affordable waterfront condos (not beachfront - it's mostly lava along there) on vrbo.com - some as little as $700/wk. No recommendation since we ultimately rented a house. I don't know if it's still the case but last summer vacancies were high - several ads mentioned offering a discount so they could get renters. fwiw USAirways has a 5+hr. non-stop flight directly into Kona (KOA) from LAX.
Anything in the Kahuluu or Keauhou area seemed like the best bet. The closest properties just south of Kona would be walking distance to some of the restaurants. Our house was just across from White Sands Beach - from there it was a short drive along Alii Drive back to Kona. If you plan to do any shorediving, the majority of dive sites are nearby:
Scuba Shore Diving Site Listing for: The Big Island, Hawaiian Islands
There were also less expensive condos near the golf course farther south but they seemed to be ocean view and not waterfront.
We also briefly looked at properties farther up the Kohala Coast but that's more of a drive. I stayed in that area once some years ago but it was a longer drive to Kona than I would want to do daily. And would add drive time to a round-trip Volcanoes ride. There's some big hotels in that area - Hilton Waikoloa and others. I think there's one dive operator that has a boat up there also. Better beaches also iirc.
fwiw, the Volcano is at elevation so no-fly/altitude rules apply there after diving.
Everybody we looked at seemed to be $125/2 tanks. I suspect that's the going rate there.
My buddy dove with and really liked Kona Diving Co. - they offered $470 for 5 2-tank dives. One to definitely do is the Manta Night dive. You can make it one of your five for $10 more.
Another option we liked the look of was Wanna Dive Kona. They offered a $15 discount starting with the 3rd charter. [user]friscuba[/user] here owns it.