According to The Vault wiki's "Lucullus" (the ferryman) article:
He is responsible for ferrying the Courier between The Fort and Cottonwood Cove. If he is killed, the player can take the raft to The Fort without him.
So you should be able to get there even if the ferryman is dead.
You can only activate the raft by clicking a specific part of it from
the looks of it. It would only work when I put my targeting marker
over the very bottom of the raft, while staying on the dock (so
basically looking straight down).
Try not actually standing on the raft, but rather while still in the docks, and try the very edge of the raft.
...stand on the docks and look at the raft. The option should appear to head to the fort, if it doesn't just slowly scan the raft until it does.
If those don't work, I'm assuming that you can't activate the raft as you haven't been invited to The Fort yet. If that's the case, have you finished the "Ring-a-Ding-Ding!" main quest? Because...
[The Render Unto Caesar] quest will begin once you exit the Tops Casino after completing Ring-a-Ding-Ding! Vulpes Inculta will approach you and inform you that Caesar wishes to meet with you. If you previously killed Vulpes Inculta at Nipton, Alerio will be there in his place. Either way, he (Vulpes or the representative) will give you the Mark of Caesar, which allows you to safely travel through Legion territory. This is essential if you have a poor reputation with Caesar's Legion. He will also mark Cottonwood Cove on your map.
Note that if you already have the Mark of Caesar before you went postal at Cottonwood Cove, (from The Vault wiki's "Render Unto Caesar" article):
If you become vilified by the Legion at any point during this quest, it will fail and the free quest Beware the Wrath of Caesar! will start.
You won't be able to continue with the main questline for the Legion if this is the case.
However, you should still be able to go to The Fort from Cottonwood Cove (from The Vault wiki's "The House Always Wins II" main quest article):
If you've once again become vilified with the Legion, or simply don't like the Legion, you can still complete this quest.
The first option is to disguise yourself as one of the Legion. Don't take your companions as the guards will notice and a shootout will ensue. Make your way through Cottonwood Cove to the Fort as normal. Speak to no one but the dock officer and avoid all legion dogs or else you'll be caught. Make your way to the bunker. The guards inside will recognize you, but they can be killed without alerting the rest of the camp as long as you remain disguised. Complete the mission as before and return the way you came.
The second option is to simply kill everything in sight. Instead of speaking to Cursor Lucullus, whom you'll have killed, just target and activate the raft to get to the fort. Kill everything between you and the bunker and complete the quest as normal. You don't have to kill Caesar if you don't want to.