PET or Polycarbonete would both work well.

Most 3d printable plastics come in a transparent version.
As long as you made sure it was watertight and not subject to the solvents used in the perfumje - absolutely no reason you couldn't make one.

The best approach would probably be to use a glass bottle and a 3d printed plastic top/adaptor to fit it to the atomiser.

Pla would also work well - I use a fair bit of transparent pla.
You also get different translucent colours in most plastics.