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Normally, meshes should use meters as their length unit (as specified in REP103). It is then straightforward to just model the part and to use it for a URDF model (or in gazebo) without having to care about scaling. If your other meshes are not given in a meter scale, you have to get the scale factor from somewhere.

You should be able to import your .dae mesh to most 3D modeling programs and edit it, but unfortunately there is a quite high likelihood that something goes awry during import (at least when using textures and similar 'advanced' stuff). For example, importing your .dae example mesh didn't work with blender 2.63 for me. It can be opened using Meshlab however. Converting it to .3ds using Meshlab and then importing to Blender worked (but the geometry is very large, so I assume the nxt parts do not use meters as their length unit, or something went wrong during the conversion process).

If you want to look into modeling COLLADA using Blender, this post documents some of my experience with that. :)