Hi,
First don't watch Firefly - it's Joss' badly flawed masterpiece, and part of its flaw is that it has no realism to it. You have no idea of how any of the tech on it works, starting with the drive, and you also don't know if they're travelling through the planets in one system or between the stars.
How to disable. Before you ask that ask yourself, how do they even find the ship in space? Space is big - mind bogglingly big - to quote Hitchhikers. Finding a ship in a solar system is probably harder than finding the proverbial needle in a haystack. Much harder. And if you leave the system that problem becomes a billion times worse. You need some reason for the ship to be in a specific location within the system - hyperspace conduit tubes (like railway lines), jump points which everyone has to use. Or failing that some super tech.
Next I would go for the power. Don't shoot holes in the ship - that'll just lead to large areas of the ship being depressurised - and I don't think slave's will get space suits. My thought would be some sort of EMP. If life support goes down, no one's going to die instantly. They can probably survive at least a number of hours, maybe many days, simply on the air that's in the ship, and by wearing warm clothes. Remember the crew of the Kirsch were assumed to have survive until nearly a week later.
Also destroying the power means they can't call for help.
Next step is boarding through a hatch. Yes they might be expecting you, but if you're armed and armoured, perhaps have some mechanical marines, and they're a freighter crew, the advantage is yours. How do you think the Somali pirates keep taking ships? Small arms all the way. They face no opposition. Freighters are unarmed by international law.
Now if space law allows freighters to be armed, the chances of piracy being successful become very small. Every gun battle even if your pirate vessel is much better armed, is a risk for the pirates, and the chances are that there will be no reward since the chance of survival of the freighter is very small. You'd need a new career.
As for shooting the engines off, unless the engines are completely external to the ship, you'd lose the ship. You might be able to use directed laser strikes (pin point accuracy) to shoot off hull mounted equipment - which would I assume include communications arrays and sensors leaving them blind, deaf and mute. But the EMP should do that for you.
As an alternative strategy I'd suggest having a co-conspirater on the planet where the ship leaves from who can send routes, manifests, defence details etc to the pirates and maybe arrange some sabotage.
Cheers, Greg.
Hope that helps.