Appreciate some folks initially don't feel comfortable in unknown territories on their own although some might by kayaking and jumping in themselves and we are true water nuts for the most part but for us seeing the Crocs on banks as we boated out and so on I'd never get my hubby to go out solo after that with me alone (LOL).
We've done the encounter with BirdsUnderWater twice and found for the price and their knowledge it was more than a good deal to us. We did one in a July (very few to encounter and distant the odd one we did find) and one in very beginning of Nov 2009. The area they took us into at very beginning of November was going to be out of bounds to protect the Manatees season from 9th November so we timed it perfectly, and we were very blessed to have the most wonderful experience and tons of manatees and babies on that trip = way better than our July experience a few years earlier. One seemed to enjoy a girl gently scratching it under it's flipper for a considerable amount of time. Ironically our guide told us thats where the nipple is and why she was enjoying it.
It's a truly wonderful experience to be up so close and personal - do it now while you can as one does wonder when it will be banned altogether.
For the Keys, we like John Pennekamp which we prefer to head out from for our snorkelling and diving and Bahia Honda if you can get in there!