Moving East to West, as you will be:
1) Stuart - Manatee Pocket has a number of marinas
(a little pricey) and anchorage.
2) Get up and around the big corner just into the river area, by the roosevelt bridge, there is Harborage marina. I stay there rather than manatee pocket anymore. Good Ruben sandwich at the bar, too
3) Heading into the waterway, not a heck of a lot for cruisers until Indiantown just a few miles from the E. end of the lake and Port Mayaca lock. Call ahead for reservations, not a ton of transient room. You can also anchor just outside the entrance if they are full.
4) After crossing the lake, the city docks at moorehaven as mentioned are an option and the closest place on the w. end of the lake. (I've never stayed in Clewiston, so not familiar with that)
5) Couple little places along the way from there headed W., but once on that side you should be good through say Ft. Myers City Marina in downtown Ft. Myers. Good stopover/marina/fuel/food etc.
Hope that helps.
Have a good ride,