If you are literally just filing the numbers off of The Scar, I don't think you'll need to worry too much about boat travel except in unusual circumstances -- the Armada contains numerous hardholds already, and is basically self-contained to the point that once you get on it, you mostly just don't get off. I would say that the extreme density of holds and people is a much greater obstacle to the viability of the Driver than the car = boat swap (the last Driver I played used boats, it worked flawlessly.)
Part of what makes the Driver interesting is his/her ability to move more freely between 'holds/places of interest. If the vast majority of your places of interest are interior to this pirate flotilla, and it is as densely lashed-together as the source material, it will require some additional effort on the MC's part to make sure that having a boat (and being a badass while in the boat) is a major resource. So emphasizing off-flotilla contacts & resources, for example. The problem here is that if they are truly off-flotilla, none of the other PCs might have any interaction with those resources/contacts at all, which really neuters a lot of the dynamic, NPC-triangle-potential that usually comes from the Driver moving all over the place. I'd say overall it would depend on how the Driver's player saw the character operating.
Chopper seems an easier fit, as a sort of raiding/roving gang that helps keep the flotilla supplied -- though the Driver could fill a similar role, minus the overt violence, operating as a go-between for important political/economic negotiations.
I would not try to keep the Chopper both 'on land' and on vehicles, but obviously that's your (and the player who chooses the Chopper's) call -- I think honesty will soon demand far more places that actual bikers 'can't go' than you would run into in a land-based game (though I guess like super-mobile dirt bikes could be awesome.)
On the other hand there is really no reason that the Chopper's gang needs to have vehicles at all; they work just fine as a gang of toughs wandering the streets, or on pogo sticks, or flying with psychic powers, or whatever makes sense. As long as they still have something similar to the 'out' that driving off to the next town provides -- and in a populous, politically-dynamic-enough flotilla, it seems like there would always be a neighbourhood/holding willing to take them in in exchange for their 'physical labour'.