it seems I have a knack for acquiring stupid/silly modding projects, and the latest suggested by my friends is one for a companion deathclaw...

so anyway I got to working on it, but I do not know how to do what I want to do. Is there a program that I can use to modify/make custom animation files with?

i want to make him dance, could i use nifskope for this?

also, how could i give a top hat and a monocule?

Learn Blender. Grab some Niftools. Nifscripts and pyffi. Also you will need python.

Start here maybe:
http://niftools.sourceforge.net/wiki/NifTools

For help with Blender search for Blender Noob to Pro. Blender Noob to Pro is a free resource you can use to learn just about everything related to Blender.

Edit: Check this out.
http://niftools.sourceforge.net/wiki/Blender