The way I'd do it would probably be:
- Put the molecular geometry into Avogadro
- Set up the view to be exactly the way I want it
- Export to POVRay, not rendering but keeping the input file
- Work out which atom is which in the POVRay file
- Add vectors using cylinders and cones (probably using a macro to define a vector to make it easier and visually consistent)
Avogadro can also render sequences of XYZ-formatted input to animations using POVRay and ffmpeg, but it's not something I've tried since I'm using Windows at the moment and Avogadro doesn't seem to have an option to specify where the povray executable is if it's not in your path.
Again depending on whether you are a Python aficionado or not, you may alternatively be able to set the forces on the atoms using the Avogadro Python console and then use the force vector display in Avogadro, but that's not something I've tried either.
I'm not aware of any perfectly convenient tool that lets you put in vibrational parameters directly and visualize or animate them, though.