One of the locations I play music at is Hyatt Place, which now stands where the old Farro Blanco Resort once stood. Hyatt has a nice marina on the Gulf side of Marathon, but it's pretty pricy. They also own the old Boot Key Marina, which is a very large facility that went out of business many years ago and is quite run down at this point. Hyatt intends to restore that marina this year and it should be ready by late fall. That will add a lot of new slips to Boot Key Harbor.
Central to Boot Key Harbor is the City of Marathon's City Dock Marina. It's about 1.5 miles to the Publix and Wynn Dixie grocery stores, K-Mart, and loads of restaurants. The marina itself holds about two dozen boats, while in Boot Key Harbor the marina manages 260 mooring balls that go for $300 a month. The only restriction is you must be a live aboard and your boat cannot be untended for more than 7 days.
There is a large marina at Sombrero Resort, which also allows live aboards, but not as restrictive as the City Dock. Lots of sailboats there, too and the price is less expensive.
The main mode of transportation here for cruisers is bicycle and dinghy. There are some restaurants and stores with dinghy docks, and everyplace has a large bicycle rack.
The entire island is only about 6 miles long and less than 1/4 mile wide, there is a large bicycle/walking path along US Route 1 and many of the side streets have similar paths. There's a small hospital and several walk-in clinics on the island if you have medical issues requiring attention. There's also an airport that has rental car services at the upper end of the island and Island Taxi will take you anywhere on the island for $5.
I have a friend that frequents Marathon Marina and Boat Yard, which is situated at the western entrance to Boot Key Harbor. He loves the place and loves to watch those beautiful sunsets every evening from the cockpit of his boat.
You'll find four good marinas at Key Colony Beach, which is situated just above Vaca Cut at the eastern tip of Marathon. They all have quick access to the ocean and very well protected from winds and storms from all directions.
I suggest hopping in your car and driving down to Marathon, spend a few days looking at the various marinas, restaurants and other features the island has to offer. It's worth the drive, especially this time of year when things are really jumpin in the towns.