Simple answer - you can't. The Niftools import/export tool for Blender is not yet equipped to handle Skyrim nifs.
What you'll need to do is import your .obj, make your changes, add material and textures, do your UV mapping, then export again as an .obj. From there, open a similar nif in Nifskope, highlight the NiTriShape/Strip and import your .obj file over it. I say similar nif because you can't change the collision, so find a nif with collision that will fit the new .obj. You'll need to adjust some of the nif's properties such as the BSLightingShaderProperty (material) and BSTextureShaderSet (textures).
Here's a http://tesalliance.org/forums/index.php?/topic/4634-3d-craftworks-importing-weapons-into-skyrim/ that explains it in more detail (it's for converting weapons but the same steps apply).