Well let's give the answer before it gets more heated. The answer is a mix of all 3.
Yes, the reflection of the blue sky helps seeing the sea/lakes blue. Nevertheless that doesn't explain then why it's not the same blue for lagoons and deep seas, or why swimming pools are blue. By the way many swimming pools have a white bottom, and if you go a few meters to the bottom and look up to the ceiling, still blue.
As many said, water is indeed blue. A very faint blue, which is why your glass of water is transparent. As the depth increases, it gets more and more blue. The reason is that water molecules reflect blue light more than all the other wavelengths (or absorb it less), as shown on this absorption spectrum :
http://3.bp.blogspot.com/_fa6AZDCsHnY/S ... rption.gif . You can see that there's quite a small difference between the absorption of blue and the absorption of yellow/red/etc... (infrared and far ultraviolet are heavily absorbed, but not near UV which is why you still need sunscreen during a swim) This small difference explains why you need a great thickness of water to "enhance" it. And that property is simply due to the water molecule itself, nothing else. Each molecule has a specific absorption spectrum, giving it its color in bulk. Use a light having its blue component removed on a pool of water, you're gonna see the water green.
Now scattering on particles in suspension in the water also helps giving it its color. Rock flour for turquoise lakes as many said, through scattering processes, some algae make it green, pink, etc...
But the explanation many don't know is that water is naturally blue. It takes a few meters of water to see it, just go in a white bottom swimming pool, immerse yourself, and look at the bottom, then look at the walls. You'll see it's more blue in the second case because light has traveled a thicker layer of water. You can see the effect here :
http://www.youtube.com/watch?v=M9GRiXBS0e0 the first swimmer on screen is lightly blue, the last one is a deeper blue. Still think it's because of the walls or the bottom ? Have you ever seen an underwater documentary where the water isn't blue ?
And here's a picture for SonofaBeach, of a river, taken on a clouded in day. The water near the bank is clear, because shallow, and as you get deeper, it gets blue (of course in this one there's also rock flour giving it this turquoise color).