The best ship, if you intend to *cheat* is the Borg Cube. Which can be received at the start of the game through an Easter Egg. Go to the Start Game screen and press TAB until you see a little yellow box appear near the Y in Play Saved. Hold down SHIFT and click on it. The screen will read "Resistance is futile.". Continue like normal. If you don't wnt to cheat, then the best ship is the Galaxy Dreadnought which can be bough south-east of Paso for about 230 000 latinum bars.
I'd actually say the best ship is the Klingon Neg'Var. This excludes the easter egg ships such as the Galaxy-X of course. The Neg'Var, when fitted with cutting beam, plasma torpedo, and particle beam becomes uber powerful. ;D