Point Cloud to STL File
In order to properly get an STL file out of a point cloud, you'll need some tool to help triangulate the points to create proper vectors. The shell that is created in an STL is what the slicing engine will "slice".

I'm not as familiar with the full potential of MeshLab, but I would think this tool is best suited for files that at least have most of shell already in place. Essentially best for fixing STL's.

In the past, I've used (the very expensive) Unigraphics NX8. This CAD/CAM software is very powerful and has tools for creating meshes out of point clouds. I believe it was the sew tool that allowed me to do this in the past (I no longer have access to the software). Other CAD programs such as SolidWorks, Rhino, AutoCAD, etc. might have similar features.

Alternatively, I think it looks like you might be able to convert a 3D point cloud in SketchUp. If the cloud is layered by height and each layer had points on the same -Z- plane, then you might be able to automate creating lines between the nearest points on the same plane. Then it might just take a little bit of manual labor to "fix" the model to become 3D printing ready. Also check out this forum post, it looks like someone had luck in converting terrain point clouds.

Completely alternatively, have you considered converting an image to STL? I've done this many times before and it turns out quite nicely. If you can find topographical map of the lake, you could alter the image into grayscale (play with it a bit). Then use software to convert the grayscale image to STL.