Air Guinee may operate between Freetown and Conakry. Not sure, check their website. But, be aware that the airport associated with Freetown (called Lungi airport) is way the heck out of town, you normally take a helicopter (USD $35) from the airport to the helipad in downtown Freetown, beside the UN compound. By road, it's almost an 8 hour drive from Lungi airport to downtown Freetown. No-one, not even the locals, makes the trip by road.
There are ferries that run between Conakry and Freetown. The schedules are somewhat erratic, and the level of safety is NIL, but if you have a vehicle with you (moto, LandCruiser), the ferry is probably the only way to go.
To put things in perspective - air transport in that region is so difficult, the organization I work for operates their own private aircraft just to move people between the two cities.