What are you looking to see and what time of the year are you looking to go?
The Tuamotu Archipelago is where you may find arguably the best diving in all of French Polynesia if you are looking for clear waters, lots of fish, and big animals. The two atolls recommended earlier - Tikehau by ACHiPo and Rangiroa by jameseg - are both in the Tuamotus. There is a third atoll in the Tuamotus that is very popular and also offers excellent diving, and that is Fakarava. Within Fakarava, there are two villages - one North and one South - and a pass at each, about 1 1/2-2hr boat ride one one another, and both passes offer excellent diving.
In Tikehau, the best diving is also at the one pass there. In Rangiroa, there are two passes, but Tiputa Pass is the one dived most often and offers the best diving of the two.
That is not to say that the diving is only good in the passes. The outer reef in North Fakarava has almost daily manta sightings at the cleaning stations. Tikehau also has a manta cleaning station (I haven't dived it) but it is inside the lagoon so viz is so-so at best. The outer reef outside of Tiputa Pass in Rangiroa is where I have had my best bottlenose dolphin encounters in French Polynesia.
With 14 days, doing all three of those atolls is possible as long as you don't mind losing parts or all of two days traveling in between. And if you get the Tuamotu Pass from Air Tahiti, the domestic airline, you'll get a slight break on the airfare.
I just did this same itinerary in December but over a span of 19 days.
I've never been to the Marquesas but I hear that the diving there is also very good, except that they do not have the water clarity that the Tuamotus have.
There are seasons for certain species, and that's why I ask about your time of year.
If you want to snorkel with Humpback Whales, that can be done in Moorea, Tahiti, and Rurutu, but that is more seasonal.
Once you come up with a tentative trip itinerary, I can offer lodging and dive operator suggestions in addition to the ones already provided above.