True, most excursions for Molokini leave early in the morning and winds are generally lighter. You will find the tour offered by NCL to be fine, if Molokini is what you want to do , take the NCL excursion. If you decide to go independent, book with Four Winds II. They do the best snorkel trip whether you go morning or afternoon. An alternative would be to take a snorkel excursion that takes you accross to Lanai. Great ride, great snorkelling and you will see dolphins and from December to April will see whales as well (as you will on trip to Molokini).
Another alternative is to go out to Kanapali Beach and snorkel in the area around Black Rock (this can be done right off the beach).
If you ask locals you will hear rumors about great snorkelling near milepost 14 on the main highway . Ignore this advice. The coral was killed off by runoff from nearby plantations and the beach area is inhabited by active tiger sharks.
Have a nice trip