Depends on whether or not you're planning on taking the galaxy by force. If yes, then I would say evil is probably superior.
otherwise, I'd say not necessarily.
The short-term benefits of being evil are obviously better than being good.
but all the benefits of being good (and neutral, too) are based around fairly significant economic, technological and loyalty/morale bonuses. So whatever losses in money and production you take by choosing the good and neutral choices are made up later.
All of these are listed in the manual.
Also, you have to consider what alignment the other races are. If the major powers in the galaxy are all aligned with good, it can be a serious blow to your relations with them if you become evil.
edit: it's also possible to balance out your choices. I played one game as the Drath, who start out leaning toward good... and had an event that gave me a +44% bonus to my ships if I chose the evil option, which I did... then, later, I chose a good option that only caused me to lose some money. When it came time to choose my alignment, I was still able to choose Good without having to pay for it.