Dena - Regarding the Bora Bora motu I would agree with Wendy and seadog in reporting that I loved it. It is different from Motu Mahana in that it does not have all the comforts of home. But it is so beautiful and relaxing there. You'll just have to do each of the motus (Taha'a & Bora Bora) as you planned to find out for yourself. We've done both of them on both trips and they were all our favorite days of those cruises.
Of the 2 choices you were leaning towards on Raiatea we've done them both and preferred the Lagoon & Snorkeling. I have to admit that we are addicted to snorkeling so we chose those tours every time. You can learn about black pearl farming from the boutique's presentation onboard the ship one evening before dinner. (Admittedly it's not quite the same as being at an actual pearl farm, but the information covered was the same.)
We loved the Shark & Ray Feeding on Bora Bora. We've also done the Land & Sea Excursion there since we figured the full 4 x 4 tour would be too bumpy for us. We liked the Land & Sea and got great photo shots back down to the lagoon from the sites where we stopped in the hills.
We were unfortunate when we went on the Dolphin watching excursion. Did not spot a single dolphin or whale (in 2004 when it was whale season on our cruise). We did a back to back cruise last year and on our second week at Moorea we went on the Lagoon Discovery with Snorkeling and in addition to good snorkeling we spotted dolphins and whales.
You'll have a wonderful time whatever you choose.