IMO, it depends on your stragegy. If you have lots of planets to grab, having the per-colony cost killing your budget could kill your planet-grabbing ability just as easily as waiting for more expensive ships to build.
I've been experimenting with 2-colony-module ships for a little while, the theory being that 500-million-person colonies can pay more for themselves than 250-million person colonies, as well as grow faster. With the fact that tax is proportional to the square root of a colony's population, financially it's best to evenly distribute your population. With the fact that the same amount of population as part of a large colony grows slower than if they were on their own planet, your population growth is maximized by evenly distributing your population. Therefore, porting larger chunks of population to new colonies not only yields more taxes (meaning you can fund more initial colonies for the same total empire-wide population), but a faster population growth.
So sure you grab fewer colonies in the same amount of time right off the bat, but if there are a lot of planets, you'll do better financially 50-150 turns into the game, and grab many more planets on the 2nd and 3rd wave of colonization than you would if you focused purely on maximizing the number of colonies grabbed in the short-term.