My party is fighting at sea and we have encountered creatures who don't surface but damage the ship. I've been thinking but don't know how to fight these creatures.
You should be able to strike them from distance. Because the water is not blocking terrain (unless it is iced) it does not block line of effectDDI.
If you can't see them because of turbid water, you could dive and probably fight an uneven battle where you should make Athletics and Endurance checks in order to swim and hold breath. It is also possible that your Dungeon Master especially designed or leveraged a particular skill challenge for this event.
Depending on your party composition and selection of powers you may have some Summoning or Conjuration spell/prayer/invocation/discipline that could bring you a swimming proxy.
Teleportation powers could move seaborne creatures on board in order to be easily filleted by your melee specialists... if their weight doesn't cause the vessel to sink.
@Ananisapta suggest the use of figurines of wondrous power. Three of them have a swim speed.
The Make WholeDDI level 1 ritual and Temporary Fix level 1 martial practice allow you to repair an object that fits in a 10x10x10ft. cube. You could ask to your DM if he allows them to repair a breach in the hull that fits in the same cube. The major drawback is that both the ritual and the practice require 10 minutes to be completed.
If the ship can manage the additional load without sinking, a power that creates blocking terrain can be used to stop or delay the water from entering the breach. These powers last until the end of the encounter (or up to 5 minutes, as usual) and some of them must be maintained each round.
The Greater Stonewall Shield (a level 14 or 24 item) can create a permanent but fragile wall of 3-5 cubes.
The Water BreathingDDI level 8 ritual allows up to 8 creatures to breath water for a variable time between one hour and a whole day (depending upon the ritualist's skill check). Again, it takes 10 minutes to be performed.
The WaterbornDDI level 14 ritual (Forgotten Realms Player's Guide) does the same for a longer period of time, grants a swim speed and immunity to the pressure and cold of the ocean's depths.
Among the items, the Elixir of Water BreathingDDI (125 gp, from Mordenkainen's Magnificent Emporium) allows the imbiber to breath water for 1 hour. The Cap of Water BreathingDDI (5000 gp, Adventurer's Vault) does the same as a continuous effect upon the wearer.
As @Ananisapta suggests, the following rituals may be proactively cast on the ship in order to enhance its durability.
I'll take a different approach from @ErikBurigo's excellent answer and address the "oh crap" issue of being attacked at sea with no preparation (rituals, potions) whatsoever.
We're under attack right now. What to do?
Note: Many of these options depend largely on the niceness of your GM
And if all else fails, jump in! Fighting in water isn't preferable, but neither is it impossible. You might expend more resources but an aquatic setting probably isn't enough to turn a level-appropriate encounter into a TPK.