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They do different things, both of them very well.

Overall I'd say the serpent is more imbalanced, due to its status as a fast vehicle, its high volume of accurate mid strength firepower, durability and potential range.

The ark has the advantage of being a reasonably cheap AV13 open topped transport with decent anti infantry (and potentially vehicle) firepower, with a little bit of utility thrown in.
Alongside the decurion's move through cover, relentless warriors,and ignoring stunned results, they are still considerable challenge to some armies.

I know the ark is already powerful, but I would have loved to have seen them as a fast vehicle, allowing me to cut the enemy line and then broadside 2 enemy units.
Balanced? Probably not, but pretty cool imo.

The Necron player in me would like to have seen the 'warriors only' restriction removed - so that you could put Lychguard in one and use it as an assault transport.

I agree the Serpent is more OP, but some clarifications:

Serpent Shooting:
-If it moved 12" or more, its only firing 2 weapons
-Shurikannons are AP5, not AP4
-SLs are AP6
-Chin cannon is 10 pts, not stock
-Cannons are 24" range, same as broadside array
-cannons have "pseudo" rending - no benefit against vehicles

Also, don't the Necron boats have two arrays, plus whatever is inside? They probably can't hit the same vehicle, but are allowed to pick different targets?

Also, for jinking, its a 3+ vs a 4+. Doesn't affect embarked passengers.

Explodes results, while much more likely for the Necrons, are usually going to be much worse for Eldar. Should be 1/3 of DA squad, or half a Guardian squad. So take both a Pinning and LD, in addition to the casualties.

Necron boats are immune to s6 and nearly immune to s7, but are a little more vulnerable to Malta and Armor Bane. Serpents don't really die to anything, but s6/7 is kinda the sweetspot for ripping them up.

Serpent Shield shooting is ridiculous, sure.

But if they aren't shooting the Shield, its a single TL heavy weapon, plus a chin weapon that is, at best, 3 shots a round, less than one pseudo-rend every other round, at only 24" range.

Let's say they go head to head. Only the Serpent Shield can hurt it.
If it uses the SL for the TL, its within 36", and is taking at least 20 shots next round. Good chance they snap fire, and can only glance.
If it is a safe distance away, it can only fire the Shield, not that anything else can touch it.

If it weren't for the Serpent Shield shooting, would the Serpent still be in the same league as the Necron boat?

I'd say they would be comparable.

Ghost arks are not fast, so can only fire 1 weapon accurately if they move 6. This is a big advantage to the wave serpent. "Only" firing 2 weapons if they move 12 lol.

The ark with warriors inside can potentially fire at up to 3 different targets, but most of the time this will either be impossible to do and is unwieldy.

An ark with warriors inside is a little more expensive than a WS with 5 DA. It makes a more all round package, with both the ark and the warriors being capable.

The WS on the other hand is going to be doing all the heavy lifting, wit hthe DA usually acting as an objective capping upgrade.