I used a replacement made out of novasuede/alcantara suede-like material from redline goods. The camera flash makes the suede appear lighter in color than it really is. They do color stitching, piping, patterns, and have a variety of colors/materials to choose from. If you have any questions or need more help on replacing the shifter boot, please ask at the VW TDI discussion forums.
1 shift boot, see below for more details
The shifter boot bottom is held with a built in elastic. You can either slide the
front edge out or pull up the surround. Flip the boot up and remove the
crimp to release the shift knob. I prefer to pry the crimp wider with a
screwdriver so I can reuse it.
Pull the assembly off. Here it is flipped inside-out with the crimp and
black ring visible.
Carefully pry the black plastic ring off to release the boot.
Installation is the reverse of removal. Use pliers to recrimp
the crimp. If it's damaged then use a small worm drive hose clamp to
secure the boot or any other clamp.
I also purchased a suede armrest cover. It's a tight fit held with elastic and just slips over the armrest.
Did you find another place that sells good shift boot replacements? Please share where you found it in the Volkswagen TDI forums.