If I have a sample of some compounds dissolved in water inside a glass vial (let's say quartz). Would it be possible to get a usable measurement through this glass vial without too much absorption by the glass itself?
As EdV said, when you have aqueous samples, Raman spectroscopy is the way to go. The problem is not the container (which should not be glass etc),the problem is water. Its absorption will hide the absorption of everything.
If you ever open an FTIR instruments, you will see that there is nothing which is made of glass or quartz because they absorb too strongly in the useful IR range.