If you put in at Little Shark River, I'd suggest anchoring in the wide area at the mouth of the river, where the channel takes a 90 degree turn. Good holding there and good protection. We anchored further upstream once, but the bottom was rocky and the anchor dragged. If you want to visit Everglades City, I'd anchor near Indian Key and dinghy into town. We draw 4' 4" and barely made it over the shoal at the mouth of the Baron River, and it was tough finding a place to tie up. That was 6 years ago, though, so things may have changed. In any case, lunch or dinner at the Rod and Gun Club would be worth the ride. We found fresh seafood for sale a short walk from the Club.
Naples City Dock had moorings available for $10 a night in 2010, with a very nice restaurant in the marina.
If you enter the ICW at Ft. Meyers, a nice place to anchor is just south of the tip of Pine Island, off St. James City. We liked to dinghy into the main canal and tie up at the little restaurant on the right, just as you enter the canal. You can eat on the deck and enjoy the Florida scenery. If you are nature lovers like we are, you can anchor just across the ICW by Ding Darling Bird Sanctuary, on Sanibel Island. We spent three days there, exploring the mangroves. Saw lots of birds, alligators and manatees.
If you stay in the ICW north of Charlotte harbor, there several anchorages available. One is just north of the Boca Grande Causeway swing bridge, another is at the wide part of the ICW at Don Pedro State Park (do not enter the small channel into the park), and a good spot is just inside Stump Pass, to the south of the channel. The Engelwood area has transient slips available at Palm Island Marina and Royal Palm Marina. The shuttle ride from Palm Island Marina to the restaurant on Palm Island is a good side trip. The next major inlet north is about 15 miles at Venice. The Crow's Nest Marina at the Venice Inlet also has a very good restaurant. From there it is a day's sail to Tampa Bay, or you could continue up the ICW. Have a good trip!
