This would be a new structure with a fixed floorplan.
An uncommon structure, overall about as rare as NPC villages. It would spawn only in Ocean Biomes (not in Deep Oceans).
Not all potential lighthouse spots, would lead to an actual lighthouse. First, a coordinate is chosen. If the water level is 2 or less there, then the generator would choose a random spot which is up to 8 blocks offseted along both X and Z directions. If water level at that THAT spot is still 2 or less, or is on the ground, only then the Lighthouse is generated. This insures some lighthouses will be ON the shore near water (maybe even on cliff's top!) and that none would be in deep waters or too far from the shore. That final coordinate would be the actual center of the lighthouse.
Some parts of the structure could be above water or even above air that is more than 2 deep. In such a case the structure "fills in" the extra and air water blocks underneath it, with the appropiate type of stone, up to an extra 3 blocks deeper (the actual floorplan normally fills only up to 2 deep under the water level).
According to the overall style of most NPC village and temples structures, the lighthouse floorplan would be on the small size of things. It would be just big enough to look like a small lighthouse. For big lighthouses, that is the players job.
The actual floorplan is quite simple. A lighthouse is a simple cobblestone 5x5 tower with cobble walls. There is some cobblestone that is actually mossy cobblestone but only in the parts nearer the ground. the entrance is a simple 1 wide, 2 high opening without a door, but with 1 block of cobblestone stairs right before the entrance. Thus, the actual ground floor (also cobblestone) is 1 block above the outside ground.
The inside is a simple stairwell, with stairs on the sides (not in the diagonals) rising clockwise for 8 blocks. Then you reach the top, outside. A raised central pillar consisting of a pair of smooth stone double-slab, with a redstone lamp on top (thus, 1 block above eye level), and then capped with another single smooth stone slab. Around the top area, a simple cobblestone wall. A lever in the OFF position is on the side of the lamp. Thus, when it is found a lighthouse is always "off" (and thus, not TOO easy to find), but players can turn them on if they want.
No special loot or anything. This is mainlya decorative structure. The lamp readily available in overworld before having to get glowstone, though, could be seen as a good loot.