You're going to be too late for morning dives anywhere on Sunday. Porting in Kahului or Lahaina?
From Kahului the boat ramp in Kihei is slightly closer. You'll also have to be up pretty early to drive across on Monday as boats leave there between 5:30-6:30 to beat the tradewinds coming back - they're smaller boats. Or you could rent tanks and shore dive Sunday morning - most of the Maui Dive Shops have rentals - the store list is on their website. In Kihei, Maui Dreams Dive Co. or B&B Scuba are also options for that. B&B might be a good option for both.
One other option if you are driving over from Kahului is Maui Diamond II out of Maalea. I don't have any personal experience with them but they advertise smaller group diving. Most of the Kihei boats are limited by boat size to a dozen or less also - they launch the boat off the ramp daily.
If you're porting in Lahaina, Lahaina Divers has the luxury of leaving later from Lahaina since they have two 46' Newton dive boats. It's still a 7AM check-in though. They also run to Molokini in addition to Lanai (different boats) With them you'd have to dive Molokini on Monday morning - they use the same boat for their 4 tank Lanai all day trip on Sat. They dive Lanai on Sun morning also.
http://www.lahainadivers.com/reservations
Lahaina Divers also does two- tank afternoon dives. One trip is to the Carthaginian - on Monday. Or they dive Turtle Reef every afternoon. They get back at 4:30 so that would be an option even if you're porting in Kahului. It took us about 40mins. to drive to Kahana from Kahului which is a slightly farther distance north of Lahaina. On a Sunday afternoon.
Hammerheads/Molokai is out since they only do that dive on Tues/Sat.
Extended Horizons to Lanai (only) is another option there - they have a smaller boat so it can be more crowded if full. I'd guess some of your fellow cruise pax might be on either one - depends on your arrival time. Maui Rafting Adventures is a third option if you don't mind staying wet the whole time...