You might want to check the Ohana section of ScubaBoard for more information. Just to get you started though...
If you're only going to dive 2 days and have never been to Maui before, I'd strongly suggest you do a charter to Lanai to dive the Cathedrals for one of them. Molokini crater would be the second charter most would suggest.
To Lanai the most common recommended ops are: Lahaina Divers and Extended Horizons, both departing out of Lahaina. Believe me, you want to go to Lanai from Lahaina, not Maalea as the crossing can be rough at times. Difference between them: Lahaina Divers takes up to 24 divers on big 46' Newton dive boats, very roomy. They use AL72 tanks. Geared more toward the vacation type diver, but give latitude to those with more experience. Extended Horizons puts 13 divers on a 32' aluminum boat. They use AL80 tanks. Usually the preferred choice of more experienced divers.
I'm an experienced diver but I prefer the big 46' Newton boats for a more comfortable crossing and have never had less than a 50 minute dive on Lanai with Lahaina Divers yet.
For Molokini, most will recommend you catch a boat at the Kihei boat ramp. Most recommended ops are: Mike Severns, B&B, and Ed Robinson's. All use comparable boats and run comparable operations, with small differences between them. For instance, Mike Severns will give you a "marine biology lesson" during their dive briefings. B&B takes quite a few students on their boats and does a great job with beginners. Ed Robinson's is geared toward the more independent and experienced diver.
For shore diving (which is a good option), you'll definitely want to check with Shaka Doug. He gets the nod here more than anyone, though Maui Dreams and Pacific Dive also get good reviews.
A few things to know. 1) Maui charters depart EARLY since the trades pick up around noon. 2) Dives are DM led. 3) There aren't really any "bad" operators on Maui. 4) October is a pretty "dead" time, so you're likely to not see any crowds on any boats. 5) Be prepared for a totally different topography than just about anywhere else