The siege weapon doesn't see its target,
but the aimer might
Who makes the attack roll?
According to the rules for Siege Equipment (DMG 255-256), siege weapons:
require creatures to move them, as well as to load, aim, and fire them.
The rules themselves provide the to-hit bonus for the weapon, but crucially, they do not say who makes this attack roll, the weapon itself or some member of its crew. To determine whose vision counts, a DM will need to decide who makes the attack roll.
It could be that siege weapons are simply objects that attack on their own. Their crew manipulate the object into position and then set it off, but it is the object itself that makes the attack roll. As objects, they do not have vision and thus would neither benefit from a faerie fire nor be hindered by invisibility on their targets. An analogy here would be a trap (DMG 120-123), which is a complex object or structure that makes its own attack rolls, after having been set into place by its maker or layer. The trap itself does not have vision, as is explicitly called out in the example of poison darts (DMG 123):
Each dart makes a ranged attack with a +8 bonus against a random target within 10 feet of the pressure plate (vision is irrelevant to this attack roll).
Because vision is irrelevant to the trap's attack roll, the poison darts would not be aided by faerie fire (or hindered by invisibility or darkness). A DM treating siege weapons as objects making their own attack rolls should rule that vision does not affect this roll.
On the other hand, it could be that a member of the siege weapon crew makes the attack roll, either treating the siege weapon as an object through the Use An Object action1, or treating them as actual weapons 2.
Siege weapons typically require three or more actions to use, specified as loading, aiming, and firing. These actions might be performed by one creature over the course of several rounds, but more typically a siege weapon would be operated by a crew for maximum fire rate. In this case, the vision of the creature performing the "aim" action is the relevant one. The creature(s) loading and firing don't need to see the target, they are just following mechanical actions related to the weapon itself. The aimer does need to see the target, both to adjust the weapon and to tell the firer when to fire, so it is the vision of the aiming creature specifically that is relevant. If the faerie fire on the target was visible to the creature doing the aiming, the siege weapon would have advantage on its attack roll; if the aimer could not see the target through invisibility, the attack would be made at disadvantage. A DM who has the aimer making the attack roll should rule that the vision of the aimer affects this roll, regardless of whether the crew is using the siege weapon as an object or an actual weapon.
A note on Ghosts of Saltmarsh
As stated above, the core siege weapon rules in the DMG do not state who or what is making the attack roll. Neither do the vehicle-mounted weapons in Baldur's Gate: Descent into Avernus, nor the shipboard weapons in the Astral Adventurer's Guide. However, the shipboard weapons in the Ghosts of Saltmarsh rules do say that it is the ship itself making the rolls, not the crew.
For example, in the stat block of a galley, we find (emphases mine):
On its turn, the galley can take 3 actions, choosing from the options below. It can take only 2 actions if it has fewer than forty crew and only 1 action if it has fewer than twenty...The galley can fire its ballistas...The galley can fire its mangonels.
Further, ship officers have the Take Aim action, which says (emphasis mine):
As an action, the captain, first mate, or bosun directs the crew’s firing, aiding in aiming one of the ship’s weapons. Select one of the ship’s weapons that is within 10 feet of the officer. It [the ship's weapon] gains advantage on the next attack roll it makes before the end of the ship’s next turn.
Thus, if you are using the GoSM rules, or are applying these rules to other instances of siege weapons, it is the weapon / object itself that is making the roll, and thus vision is irrelevant.
Do you have line of sight?
Note that some siege weapons fire in a high arc and as such are designed to shoot over obstacles, such that their targets may actually be behind total cover when fired upon. In this case, if it was a creature aiming the siege weapon, they would likely be unable to see the target and thus would not have advantage from faerie fire, but would already have disadvantage from attacking an Unseen target even without the target having invisibility.
A special consideration for area of effect and large targets
Faerie fire is quite explicit that it aids attacks against objects. Even better, as objects, targets would be automatically affected since they aren't allowed a Dex saving throw. DM-permitting, using faerie fire on an opposing section of fortification, naval ship component, or siege weapon would be a good strategy.
However, using it against an entire Spelljammer is somewhat problematic. Spelljammer ships, unlike the seagoing ships in Ghosts of Saltmarsh, are treated as objects 3. As "an object", one might be targetable by a single heat metal spell, no matter how large. Faerie fire, on the other hand, does not target 'one object regardless of its size'. Rather, it targets "[e]ach object in a 20' cube". Is an object that lies only partially in the area of effect affected4?
The rules for siege weapons in the DMG don't tell us who makes the attack roll. If the siege weapon is making the attack roll, vision simply doesn't matter. If one of the crew is making the attack roll, then all the effects of vision (including line of sight, Unseen targets, and faerie fire) do matter.
1In this case, they would be analogous to things like Holy Water, Thrown Oil, and Alchemist's Fire. The object is treated as an improvised weapon, and the creature throwing it makes the attack roll.
2In support of this possibility, we have the description of Daern's Instant Fortress, which says (DMG 161):
The roof, the door, and the walls each have 100 hit points, immunity to damage from nonmagical weapons excluding siege weapons, and resistance to all other damage.
"Nonmagical weapons excluding siege weapons" clearly supports treating siege weapons as actual weapons, albeit ones in which most PC's will not have a weapon proficiency.
3Despite the DMG passage cited by Dave's answer, the Spelljammer rules treat an entire Spelljamming vessel as a single object. Besides having a single AC, damage threshold, and hp, we find passages such as the rules for Crashing, which say (emphasis mine):
A spelljammer can run their ship into another object or a creature by moving the ship into the target’s space and making a special attack roll (1d20 + the spelljammer’s proficiency bonus) against the target’s Armor Class.
Saying that a ship can run into another object means that the ship itself must be an object; if it were not, the sentence would have to read 'A spelljammer can run their ship into another ship, an object or a creature...'. Similarly, while many weapons attack "one target", the blunt and piercing rams, specifically designed for attacking other ships, instead say that they can be used to attack objects or creatures; if a spelljamming vessel was not an object, it could not be targeted by a ram.
4If 'in' here means 'entirely contained within' and the entire spelljammer ship does not fit within the 20' cube, then the ship cannot be the target of the faerie fire. If, on the other hand, 'in' means that at least some portion of the object must be contained within the area to be affected, then it is not clear how to rule (similar to when a multi-square creature on a grid is partially within an area of effect).
A DM might also rule that just a 20' x 20' section of the Spelljammer is illuminated, and IMO this would work for negating the bonus of invisibility on the ship. However, in terms of attack rolls, it would mean that to benefit from the faerie fire, an attacker would have to be able to target just the portion of the ship that was illuminated, rather than the object as a whole. This is the equivalent of a "called shot", which is not supported by RAW.