I can only relate personal experience, as I am not as knowledgeable about the local area as some of the others here, but I was in a similar situation last year with my wife - "water timid" was a great way to describe her (and still is) as she was reluctant to get her hair and face wet; we connected with Alec out of the Force E Boca Raton store, and I cannot say enough good things about him - knowledgeable, patient, calming,,, I could go on and on.
Valerie (my wife) had difficulties with the mask removal tasking, and I had I had to spend several nights working with her in the pool before she was comfortable enough with it to pass; we then scheduled a trip to Pompano Beach, spoke with Alec, and he suggested Blue Heron Bridge as a starter, to get her comfortable in the water. This was probably the best thing he could have done!
Once he was satisfied with her skills, only then did we do a boat dive, where he had her repeat the skills test; after a few "tense" moments Valerie finally accomplished everything required, and we did a couple of dives in the ocean; she doesn't dive as much as I do, but likes to do shallow reefs, etc., and is slowly becoming an addict!
I think the key here isn't so much as where you do it, but the instructor that she will have; I'd strongly urge you to reach out and talk to them to make sure they understand your (and your wife's) concerns; a couple of months ago we were staying at Singer Island, and my wife had a new (prescription) mask that she wanted to try out, so I hired a guide from a local shop; I explained that my wife was timid and that we needed an experienced guide that would stay with her; things were good until we got to the shop and changed guides on us. The person we were given was a complete waste of my time and money, as all she said was "keep up"; my wife got so frustrated that she walked out 10 minutes later.
KevinL