Agree re: Marco. Great hotel and a very short drive from a kayak outfitter right on the other side of the causeway. Remember that Marco is basically in the everglades, so nature abounds. The area b/w the island and the mainland is beautiful, and you are an easy distance from the glades as well. Even on the island itself, you'll find strip malls with burrowing owls in the medians. Wacky. We stayed at the Marriott for our honeymoon in November of last year, despite the construction it was a very enjoyable and relaxing stay. Breakfast buffet is particularly great there.

That said, the "nature coast" north of tampa would also be an option. I can't say anything in particular about them, but there are Marriotts near Ocala and North Tampa that would give you access to this area. Homosassa Springs and Crystal River (swim with manatees, kayak, etc). Downside: will be chilly that time of year in comparison to Marco.

Finally, there is wonderful kayaking all over south florida, it's just harder to find among the strip malls. You can go 4 miles from Dadeland Mall (Miami) and be in the Bay in full mangroves, with unbelievable wildlife. You will, however, need to rent a vehicle that will allow you to transport your kayaks around (if you aren't coming with them).