For Manatees, Crystal River is really the name of the game. There is no other spot as reliable for consistency, numbers, and quality of interaction. My wife and I go there at least once a year (and did three consecutive dives over New Year's weekend--all were unbelievable!!).
I second Birds Underwater. It is THE class act in the area although there are some other nice operators. Birds is the definite first choice for us and had been for 10 years. I recommend it over a do-it-yourself try with a rental boat. You won't save much money, and the shop has three boats that are in constant touch with each other so as to get to the best location.
As for conditions, it is calm, no current, and pretty clear. Very mellow conditions and no worries. Water temp is 70-72F in almost all of the spots the shops go, because the manatees also prefer the warmer water of the springs. Wetsuits are essential. We dive 3 mils with beanie hoods and can stay in over 2 hours without chilling too much.
I kid you not, if you hit conditions right, the manatee snorkel is one of the most thrilling dives on the planet. It sometimes gets disrespected because it is so easy that families, kids, and non-divers partake. Still, the interaction with these huge, gentle, funny and friendly animals, who are completely wild and free and could ignore us if they wanted, is absolutely remarkable. If you are limited on time, I would skip South Florida in favor of Crystal River.
If you do come to S. Florida, BHB is also a "do not miss" dive, but not so much for snorkelling. It is OK to snorkel in the window of slack tide, but BHB is really famous for its small, weird, bizarre invertabrates and bottom-dwelling fish. You have to search for those and freediving down is very hit or miss. That is why, much to my own disbelief, I find myself scuba diving in 8 feet of water! (I am a long-time freediver, but it's just not the best for BHB). That being said, the conditions at slack tide are very mellow for about a 40 minute period and maybe your wife could scuba.
Or, even better, check with Brownies Palm Beach Divers. They might be able to rent out one of their hookah rigs that would allow you to "scuba" without the tanks. That would be a perfect solution for you!
Have fun on your trip.
This time of year, you will need a 3 mil suit and beanie for best comfort.