Just be careful if you decide to pick up the Pirate Train, as all of the Houses outlaw the use of that ship. The two ships available that are totally legit however are the Borderworld Transport and the Serenity. Both are solid choices, though I see more Serenities than BWTs. I know at one point in time, the BWT had a bug in which it was extremely difficult to dock with trade lanes, as it would attempt to enter them off-center, resulting in a bug in which you would never be able to use the lane in the first place. Hopefully they fixed that, though!
Edit: Alternatively, if you want a super-heavy armor 3600 transport, the Passenger Liner is also a choice, albeit far more expensive.