Here's my tried and tested, using destroyers. Good thing about destroyers is they have large crew and enough firepower.

First, take your destroyer and go close (within 1km) of the pirate destroyer. Scan it TWICE (right click on the pirate, SCAN). This will tell you how many crew it has. When you scan it, it will also start running away. When it runs away, it will boost and use up half its shields - handy!!!

Follow it until it's in a deserted area. If it stops just scan it again and it'll flee again.

When the time is right, fire and destroy two of its engines. Leave one engine untouched because that will reduce your repair time later.

Then, fire and destroy all its turrets except for the forward batteries. Some people say this step is not necessary but I prefer not to be shot at.

Don't shoot any of the shield generators, you need them to protect your prize from any over-eager system police.

Reduce the enemy destroyer to 60% hull. If the engines get repaired, shoot them until one engine is left.

If the hull gets this too low the enemy destroyer will start releasing laser towers. This is very annoying as the laser will cause collision problem and prevent either you or the enemy from moving later. Destroy them with your ship.

To stop your ship firing on the enemy, press enter then at the top of your turrets list, click armed->disarmed to turn off all your weapons at once.

On your ship crew menu, shift all your service crew to marines. You should now have about 50 marines. Actually they are engineers but it's ok, just give them guns and launch them over.

The enemy should be at 65% hull and it's shield level is not important. Right click, board.

The board screen will come up. Select all your elite marines to board, followed by veteran, then rookie. Sometimes not all can take part depending on the crew capacity of the target. Send your most experienced first.

At the bottom, click "very strong" for both weapons and hull. So that your marines will launch at once and not complain about the enemy still having one pulse turret or something.

The marines will launch over in their pods. Just watch the boarding screen. Some of the marines may die, but that's a sacrifice I'm willing to make. They may complain that they need to withdraw, or request to abort mission. Ignore the whining.

If the enemy ship stars repairing, let the ship repair. As long as the hull is less than 80% it's okay. The more repairs they make now, the less you'll have to wait later.

The ship is yours! Promote the worst marine on board to be the captain. Not the best marine, you'll need him to board other ships. Reassign all your marines back to service crew so they will fix up the ship. If you play it right they will repair almost everything by the time they reach the ship yard.

The destroyer you now captured is now your boarding ship. This avoids you having to transfer your crew. Every time your marines capture a new ship, that ship becomes the boarding ship. Your marines will soon be 5 stars.

Send both destroyers to the nearest 20 rep shipyard to top up the crew and swap out bad modules for good ones.

Don't forget the most important step: right click your new destroyer, then redesign. Now swap out the scale plate green paint job for your own faction's rocking paint job.