How many boarding pods per ship do you think is good?
As mentioned by Rico, it depends on the size of the target, and whether or not the target is equipped with boarding pods. You get about 20 boarding defense per habitation module, and in general you'll see about one habitation module per 100 size. The size of a target ship can be estimated by visually comparing the size of its sprite to the size of your own ships' sprites. Boarding assault strength starts at 50 per pod, and goes up to 100 per pod. I would try for at least 50% more boarding assault strength than expected boarding defense, so an early-game 200-300 size destroyer might be something that can be taken with two or three boarding pods, whereas a large capital ship might take so many as to be impractical to assault. You can get an idea of how powerful the boarding defenses of a target should be by opening up the ship design screen and creating a design of about the right size (you need not save this design), and checking the 'boarding defense' line in the 'defenses' box in the lower-right corner of the ship editor.
Also as mentioned by Rico, the capture order is available in the orders menu you can pull up with control + right click, but only if there is at least one boarding pod available in your fleet. Boarding will also occasionally occur during normal combat as an opportunistic action by a ship equipped with boarding pods, and can be available for selection when right-clicking on a destination (offered as a capture some specific thing near the destination, similar to the attack/prepare and attack order). Opportunistic boarding during normal combat should not be counted on to secure a vessel for you. If you want something specific, then you ought to manually order its capture by at least one ship with available boarding pods, preferably close to the desired target. Also be aware that it can be beneficial if the boarded vessel jumps away, as it can no longer be subject to potshots from your nearby ships, and likely will not be in close proximity to enemy vessels if your boarders successfully seize the vessel, but on the other hand jump inhibitors are almost essential if you want to capture something with a fast-initiation hyperdrive (especially late-game Kaldos, Velocity, or Torrent drives).
Boarding ships and squadrons also need to walk a fine line between having too little firepower to break shields and having so much that the target vessel is severely damaged by the volleys that bring the shields down, especially if the target vessel remains in firing range of the host vessels of the boarding pods, as they will send potshots at the boarded ship every time its shields regenerate beyond a certain limit, and these potshots are not necessarily calculated to only bring down the shields, particularly when you have a squadron of ships each firing off some potshots. Also make certain to check your empire's policy regarding boarded vessels: you may find that the computer will scrap boarded vessels - either immediately for cash or at a shipyard for research and a few resources - if you do not have the correct policies set.
Also be aware that if you want to capture a ship while engaged in a battle with other vessels in the area, or if you try to capture a group of vessels in the same area at once, that boarded vessels may continue to fire at your own ships while the boarding actions are resolved but will generally take only intermittent return fire when their shields recover beyond the boarding threshold; this can endanger your boarding vessels or cause them to suffer unnecessary amounts of damage. It may be somewhat advisable for boarding vessels to focus more heavily on a strong alpha strike and powerful shields than on sustained firepower, just remember that they ought to be fast enough to run down their targets in case the target tries to flee and still needs to have enough sustained firepower to deal with shield regeneration and overcome as much of the shielding as is left over after the alpha strike. Beyond that, unless you chose to create a special design specifically for boarding actions, your boarding vessels need to be viable in normal fleet actions as well as in their boarding role. Another note is that ion cannons may be relatively more useful for boarding vessels than normal vessels, as ion cannons disable components rather than outright destroying them.