I'd also vote Hound, it's the ship that best encapsulates the themes and feelings that Starsector is trying to evoke. Adventure, making do, struggling against overwhelming odds, suspending the decay, combat&trade, it's all there. It's a real shame that it became kind of a joke in actual performance, it used to be pretty good. I wish we could find a new cool niche or job for it, other than "cannon fodder" and "freighter, if you got nothing better at hand".
Also, it has the best art:
Place two are shared by the Hammerhead and the Onslaught, in my mind.