Is this question limited to modeling only, or do you also want to manufacture that shoe last. And if you want to manufacture it, by what means ?
If you have a 3D scan, the first thing I'd check is for scanning defects. Holes in the mesh, undercuts that should not be present etc. Those I'd fix probably with Meshmixer, or Meshlab.
That mesh could be exported as an .stl file. .stl files can be machined directly in Fusiosn 360.
That of course would resemble a machined foot and not a shoe last. At the very least, you'll have to "do something" about the toes and hand/model something.
At that point I'd likely re-mesh, or re-topologize the mesh. My preference would be retopology as that yields a mesh with better topology as opposed to a remesh. You could use TopoGun ot the blender plugin RetopoFlow2 for that.
Or maybe you are happy with re-meshing. Then you could use Autodesk Recap or InstantMeshes.
The remasters in ZBrush and 3DCoat are highly regarded.
Then you might want to "do something" about the toes in a mesh modeling application. You could use any of the commonly available Sub-D polygon models for this. Blender, Cinema4d, MoDo, 3DS Max. Maya etc. Each of these apps have their unique strengths.
Or you could import the remeshed result as a quad mesh into Fusion 360 and convert it into a T-Spline and then make the edits there.
This is just one out of a number of possible avenues.
You could also import the .stl into Spacelaim or Geomagic Design X to create NURBS surfaces from the .stl directly. Not exactly low cost options but very capable.
Or you use Cyborg 3D Mesh to CAD to convert that quad mesh into a NURBS surface and then use it in in Fusion 360.
Maybe you like Solid Thinking Evolve and use their PolyNURBS technology or this.
The question what is THE best application is the wrong question, because it assumes that there is one application that is good at doing all of it. That is not the case. The limit is often not the app it's knowledge and skill.
