I probably sound like a travel agent but for years we had inexpensive direct flights to Hawaii so I've been there a few times.
For Molokini you might want to stay in Kihei or more expensive Wailea. Everything from affordable condos across the street from the beach to the Grand Wailea or Four Seasons resorts are options - priced accordingly.
Almost all the boats going to Molokini leave from the Kihei boat ramp but there's nothing nearby.
We rent condos in Wailea. Most have a beach/beachfront access and are mixed in with the larger resorts. Since they're on separate bays, you hardly notice. Several of the beaches, Wailea, Polo, Ulua are also known shore dive sitees. In Kihei Maui Dreams Dive Co. specializes in shore diving and can provide paid guides or info/tanks to DIY. It's legally required to tow a flag - we never have. You might also contact Shaka Doug - you two would get along fine.
www.shakadivers.com
Maui Dive Shops also have several locations on the island for rentals, they also sell a fill card and have a free shore dive pamphlet in the stores.
Most of the boats leave the ramp early and do 1-2 dives off Molokini b4 heading back around noon. Some do a dive off south Maui also. Inside the crater is nice diving, the edges a little deeper and the Backwalll more sporty - often a live drop and drift dive. Big pelagics will share the dive with you and the bottom is about 3-400' down.
Operators to consider (there's many - these are just some I have experience with)
Mike Severns Diving - all naturalists so you learn something on the ride over.
B&B Scuba - just nice people run it.
Ed Robinsons Dive - Ed has been diving for years. They do more advanced dives certain days of the week. Once my buddy did their 3-tank and the 3rd dive at the flap-flap cleaning station off Umekahame Beach. Not as good as Kona but they saw 3 - in daylight.
The other thing to do is drive to Lahaina (or stay there and drive down to Kihei) and go out to Lanai. It's 45mins. to an hour even at 6am.
The Cathedrals are the other signature Maui dives, Lahaina Divers does a once a week Molokai (not Molokini) Hammerhead dive and I like the West Lanai drift diving. At one site in fairly shallow water we saw 4-5000 tangs and butterflyfish holding n the current while we flew past. And a dozen white tips circling the edge.
It's really rocking out there sometimes - they'll want an advanced cert. or equivalent experience.
Extended Horizons also does similar dives on a smaller boat and guides at Mala Pier off West Maui. Mala should be on your must do dive list.
Other fun things on Maui. Daybreak at the observatory - watch the sun come up then get on a bike and ride down the volcano. There will be a lot of people doing it and they follow with chase cars if you have a problem.
The helicopter rides are good. They go up the other coast where there's basically no roads - or to Hana which is one of the twistiest roads in the world to drive. Takes all morning and you can stop along the way and play in the waterfalls.
We liked Blue Hawaiian helo's but there's a couple options. Not cheap.
Kaanapali Beach is nice but crowded. Kapalua Beach is one of the nicest on Maui. Kaanapali has jetski rentals and parasailing off a boat. Even tandem kites. It's fun and you go high enough to get a great view of the area.
There's about 4-5 malls for shopping. Whalers, Kahana Gateway, Wailea Gateway and one I don't remember the name of. Lahaina town is blocks of shps, galleries etc. Wailea is more upscale.
If you golf, do the Ocean Course at Kapalua. Or either the Wailea Blue or Gold courses.
One restaurant worth the drive is Mama's Fish House in Paia. It's on the NE side. Nicer than the name suggests and you can watch the kitesurfers while waiting for a table. There's also a couple nice places to eat along the boardwalk in Kaanapali - I dpn't remember the names.
Kaanapali/Kahana are the big resort areas- - some big condo rentals as well as resorts. Makes the area a little congested. We've stayed in condos in Wailea - Wailea Ekahi and a property in West Maui in Napili Bay - kind of an older area with smaller complexes - many beachfront. Next bay over is Kapalua - nicer condos and expensive shops.About 10mins drive to Lahaina.
Kona is kind of 3 distinct areas. One is Kona/Kailua which is near the airport and the dive boats which all leave from Honokahau harbor. Lots of resort/condo options south of Kona town for several miles - most waterfront but not beach front as the beach there is lava - and sharp. Seveal shore dives in that area.
Most of the dive shops are in Kona. 3 in the same industrial mall on the east side. You go there, sign up then meet at the boat all week. We like Kona Diving Company but there's also Big Island Divers or Jack's Diving on Alii Drive south of town. Kerry at KDC would get your sense of humor - she's fun.
All do the flap-flap dives, Jacks also does Pelagic Magic and all dive south which is where you'll likely run into spinner dolphins besides all the turtles. The extended range trips some do around the Red Hill area are supposed to be best.
Obviously the big other draw on Kona is Volcanoes National Park - currently singeing a portion of the island. It's a long drive south so plan on all day. 45 minutes drive north of Kona is the Waikoloa resort area - the Hilton there is it;s own little world - including dolphins and a stand up paddleboarding lagoon. Two shops keep boats narrby - Kohala Coast and Waikoloa Divers.
Supposed to be some good shore dives off Puako farther north - and a couple of private guide options in the area. From there you'd have to drive down for the flap-flap night dive.
If you are in that area for dinner - Roys Waikoloa is recommended - and pricey. There's quite a few other restaurants along the coast and in Kona that are waterfront also. Big Island is accurate - you'll be doing a lot of driving between things. Don't go inland on dive days at the elevation on the road to Hilo peaks at about 6600' Mauna Kea observatory closer to 13000' They'll frown on your going up there in a car so rent an SUV. Pre-book a car on Kona - walkups at the airport are a lot more expensive.
We've stayed inland in Waikaloa but it was too quiet and a drive to everywhere. Also rented a house on south Alii drive which put us a couple miles from most things. Hilo is more of a locals town with the cruise port there but don't make a special trip over. Only one shop there and one or two shore dives.
Ok,I've written enough,,,
