This is actually something I've looked for before with no luck so I thought I'd help us both out by doing some of the work myself.
The good news is that movement is vital in aquatic games and most maneuvers being standard actions allows you to move and still accomplish damage. None of the classes are that impacted by the limits of water, like an Alchemist without the proper archetype would be. So almost any Class and Discipline should be fine, except Iron Tortoise and the ranged disciplines Solar Wind and Tempest Gale.
Maneuvers themselves don't mess with the blunt/piercing/slashing damage types so their penalties will be keyed off of your weapon choice. Matching weapons that work well underwater (piercing) with the Associated Weapon Groups of a discipline can be difficult, but not using a discipline weapon isn't that big a deal. The Aquatic Combatant (or Aquadynamic Focus which requires Weapon Focus) feat negates any issues in regards to melee weapons. Aquadynamic Shot lowers underwater ranged penalties but does not negate them and has several prerequisites. As far as I know the Underwater Crossbow would be the only non-magical option for a ranged weapon. Thrown weapons don't work at all except in specific scenarios.
Many maneuvers allow trip attempts. Trips can be hard to pull off underwater since the DC is a swim check made by the opponent and creatures with a swim speed get a natural +8 and can take 10. In addition, instead of being prone, they would be off balance which can be less beneficial to an attacker than prone. Many maneuvers can knock enemies prone without tripping, so it may be best to assume they knock off balance instead.
Some disciplines have supernatural effects which isn't an issue except for supernatural fire effects. They don't work underwater unless the maneuver outright says they do.
Cerulean Seas is probably the most detailed third party aquatic sourcebook and does things a bit different than Pathfinder's official aquatic rules. My answers are based off of the official rules but I do recommend Cerulean Seas for avoiding a number of headaches if the campaign is entirely aquatic with aquatic races. e.g. Tripping and prone is handled differently, there's an alternative to thrown weapons, switching most fire stuff to steam, and many weapons are designed for underwater combat and do not take penalties such as underwater bows that make the ranged Disciplines viable.
Classes:
Harbinger
Mostly works well. The speed bonus applies to all movements, which is helpful if the character has a swim speed. Grim News at 9th and 15th isn't as great. It's a bit late for a swim speed and both the Fly and Climb speeds aren't as useful. Teleportation is still good.
Mystic
The only sticking point is if you choose fire abilities, in an Aquatic setting like Cerulean Seas I'd just switch fire to steam and be done. The specific exotic slashing weapons they get are kind of useless without the Aquatic Combatant feat, so it might be worth changing them.
Stalker
I don't see any particular conflicts, not all of the Stalker Arts are necessarily as good under water but no big issues. Alacrity is worded in a way that it should work with swim speed even though it mentions land speed.
Warder
The area denial stuff is sweet in a 3d environment but a headache to track and very limited if you don't have a swim speed. If the character goes heavy armor buoyancy will be an issue even with the class negating the Armor Check Penalties.
Warlord
No issues. A lot of Gambits work better with a good move speed, therefore a good swim speed. Sweeping Gambit is a trip and trips can be less effective underwater.
Zealot
Even without a swim speed the Zealot works pretty well under water. No need to speak and limited need to move quickly.
The only thing even marginally less useful underwater is the 10ft ectoplasmic wall from the Creation Mission.
Disciplines:
Black Seraph
Associated Weapons: Axes, flails, pole arms have few piercing options.
Maneuvers: Work fine. Lots of charge maneuvers so mobility is needed. There is 1 maneuver that knocks enemies prone (without a trip) that needs to be adjusted for knocking them off-balance.
Broken Blade
Associated Weapons: Close and Monk have piercing options, all natural attacks (and I believe unarmed attacks) work fine if the character is aquatic but otherwise have the penalties.
Maneuvers: There is a maneuver that trips. Three maneuvers that knock enemies prone (without a trip) that need to be adjusted for knocking them off-balance.
Cursed Razor
Associated Weapons: Spears and light blades have piercing options. Heavy Blades has very few if any.
Maneuvers: Works fine. There are 2 maneuvers that knock enemies prone (without a trip) that need to be adjusted for knocking them off-balance.
Elemental Flux
Associated Weapons: Light blades and monk have piercing options. Thrown is ineffective except in special circumstances.
Maneuvers: Fire attacks are the biggest victim, but you can choose what energy you use for any Maneuver, except the 9th level maneuver which uses every energy type. There are some maneuvers that trip or knock prone, but it depends on the energy type you are using.
Eternal Guardian
Associated Weapons: Hammers, Heavy Blades, and Pole arms have few piercing options.
Maneuvers: Work fine. Several work off of reach which is good, but extra work to keep track of in a 3d environment.
Golden Lion
Associated Weapons: Hammers, Heavy Blades, and Pole arms have few piercing options.
Maneuvers: Swim speed is necessary for the whole party to take full advantage of the maneuvers that allow allies to move off turn and the character's charge maneuvers.
Iron Tortoise
Associated Weapons: Axes, Heavy Blades, and Close Weapons have few piercing options.
Maneuvers: All sorts of maneuvers that don't work well underwater. Shield bashes which are usually bludgeon (7), a trip attack, throwing your shield which is ineffective (3), lowering mobility. There are still plenty of defensive and taunting maneuvers to pick, but Iron Tortoise, much like an actual tortoise, is very limited in the water compared to other disciplines.
Mithral Current
Associated Weapons: Light blades has piercing options, heavy blades and pole arms have very few.
Maneuvers: Four maneuvers have trips. One knocks prone and needs to be adjusted. Requires a lot of mobility so a swim speed is good.
Piercing Thunder
Associated Weapons: Spears are all piercing, pole arms have few piercing options.
Maneuvers: Two with trips. Two require throwing your weapon. So, piercing attacks are good but a few maneuvers aren't effective underwater even with a spear. Six with prone need to be adjusted.
Primal Fury
Associated weapons: Axes, Heavy Blades, and Hammers have few piercing options.
Maneuvers: One maneuver trips. Two knock prone. Works fine, it needs a swim speed to take advantage of charges, bull rushes, tramples, etc.
Riven Hourglass
Associated Weapons: Light blades have piercing options, flails and hammers have very few.
Maneuvers: Unhindered Step specifically does not work on Swim speeds, so is ineffective in the water. Every other maneuver should be very helpful underwater.
Scarlet Throne
Associated Weapons: Altogether, heavy blades, light blades, and spears have plenty of piercing options.
Maneuvers: One maneuver knocks prone, but everything else works well. A swim speed helps with several maneuvers that trigger movement.
Shattered Mirror
Associated Weapons: Heavy blades, light blades, and close weapons have some piercing options spread throughout them.
Maneuvers: Just one maneuver knocks prone. The rest of the maneuvers work fine.
Silver Crane
Associated Weapons: Bows will have penalties, spears are good, hammers have few piercing options.
Maneuvers: Works fine. No less situational underwater than above as it's focused on fighting evil creatures like undead and outsiders. One stance has a Fly speed which doesn't work underwater.
Sleeping Goddess
Associated Weapons: Flails and heavy blades have less piercing, monk and spears have more.
Maneuvers: Unbroken Stride would be useful near the surface, but not so much deeper in the water. Everything else works fine. The teleporting maneuvers help with mobility.
Solar Wind
Associated Weapons: Bows and crossbows have heavy penalties, firearms and thrown don't work at all without a lot of effort.
Maneuvers: Keep in mind there are variants, so you do not have to use fire damage. However, since almost everything is a ranged attack, that's kind of a moot point.
Steel Serpent
Associated Weapons: Light blades, close weapons, and monk weapons have plenty of piercing options.
Maneuvers: Works fine. I don't think any maneuvers are impacted by aquatic terrain.
Tempest Gale
Associated Weapons: Bows and crossbows have heavy penalties, firearms and thrown don't work at all without a lot of effort.
Maneuvers: Ranged attacks, so always at a penalty.
Thrashing Dragon
Associated Weapons: Close, light blades, and double have plenty of piercing options.
Maneuvers: One trip maneuver. Four maneuvers for thrown weapons. Otherwise works fine.
Veiled Moon
Associated Weapons: Light blades, double, and spears have plenty of piercing options.
Maneuvers: Works fine. I don't think any maneuvers are impacted by aquatic terrain.