You will have to forgive the lack of sources in this answer, as I am using references from a real book which I own (because I'm really that much of a nerd). Usually I'm much more link heavy in my answers.
The creature that I am using is something like a "cloud" or massive collection of gases, as referenced here. It is made up of small, organic "organs" within a larger, gaseous form. These organs are connected by electrical paths much like our own brain cells are connected to one another. The creature is essentially one giant brain, with the organs acting as cells, communicating. The cloud is made up of the same materials our own body is made up of, but on a much larger scale and in a gaseous form. These allow the brain to travel through the vacuum of space (with some minor handwavium).
This creature feeds on gaseous elements, hydrogen, oxygen, nitrogen, etc, all the gases that are found in abundance in the universe. In the short story it is based on, the creature sucks out needed replacement gases of a planet's atmosphere and leaves behind wastes (the story specifically puts Earth in danger of this creature). 731
It can also eke out pockets of gas by heating up its own body (potentially hotter than a sun) to evaporate gases from asteroids. The creature is even capable of moving through space by thrusting out waste gases to propel it forward, giving it some maneuverability.
Should your spacecraft exude some kind of gaseous waste from its engines, the Black Cloud may be attracted to it, and begin to follow behind it, sucking up the trail of waste gas. It may at first only feed harmlessly on this waste gas. The cloud would then become hungrier, and become aware of an oxygen-rich environment within the craft. While your spacecraft might be fully sealed from gases, perhaps the cloud has some gases which are radioactive, damaging the spacecraft. Perhaps even the cloud can infiltrate the engines to try and get more sweet delicious gases, forcing your spacecraft to a halt. Perhaps the cloud can heat up its body to "smoke out" the gases within your spacecraft, mistaking it for some weird asteroid. And even the solid "organs" of the cloud can perhaps physically attack the ship, seeking to expose the gases within.
Possibilities may or may not be endless with this sort of set up. 500