Hello Mark,
Arriving in Freetown at that time of the night can be a bit scary for even sierra leoneans and might leave you a bit anxious. First of please know that there is nothing to fear, what you will be surrounded with will be lots of people wanting to help carry your bags for you in hopes of getting a bit of money. No one is there trying to rob you or cause physical harm. Usually the ferry will be available around the times that the flights arrive, though I don't think you will get one that early in the morning.
You can stay overnight at a hotel nearby like Lungi Airport hotel which is less than a mile form the Airport, Or Mahera beach hotel which is about 1mile from the airport.
You can call and reserve a water taxi ecowatertaxi dot net. Call them and arrage a water taxi to be waiting for you.
From the airport if you have no one meeting you, I suggest you get 1 person to help you with your pags, and stick to that person. Usually if you use the eco water taxi, they will help arrange for someone to meet you at the airport and get you to the boat. They usually have fixed times, but I am sure if you call them and are willing to pay extra, they might make a special trip to pick you up. They depart from Mahera Beach.
If you use the water taxi, make sure they take you to Alex's Beach bar destination, it is much closer to Country Lodge. Remember Country lodge sometimes have problems accepting credit card payments, and sometimes only deal with cash. Bring enough money to pay with cash for 1 night, then the next day you can just go to the bank and get money out. It is much safer than carrying a lot of cash around with you.