Sounds like fishing from a houseboat would be a really cool way to enjoy fishing the Keys.
If it was me, I would concentrate on drifting the grass flats of Florida Bay for trout and any other fish that happens along. Depending on conditions, you will probably get some good drifts allowing you to cover a lot of ground. You can put out some live baits on corks and cast artificials as you cruise along – sounds like Kokamo
Conversely, I don’t know if I’d want to be tarpon fishing on a houseboat in a busy channel near a bridge.
Whatever you decide to do, come back and tell how you did.
"I would rather have a German division in front of me than a French one behind me."
--- General George S. Patton