I think you may be disappointed in Naples/Marco water quality...head for the Keys if that is important. Also...you are leaving it rather late in the season if you are crossing the gulf directly. Northers can really spoil your day in the open Gulf. You may wish to consider a more coastal route.
If you do want to stay on the west coast of Fl...suggest Ft. Myers as easier to navigate and more boater friendly with city moorings for rent and an easy walk to the beach and stores/shops.
This would be a good guide for your trip...