Water is problematic. The 940nm light is partially absorbed by the water, and whatever is not absorbed tends to goes through the water, hits the bottom and bounces back. And of course the light slows down as it traverses the water. So clear water does NOT work well.
Turbid (dirty) water, or aerated water works well as the light bounces off the surface as expected.
(As a side note, 940nm light is partially absorbed by the water vapor in the upper atmosphere, which is why we chose that particular frequency.)
What to do...
1) You can try the VL6180V1 or VL6180X. Both use 850nm light, which does not penetrate water. But the 6180 devices, don't go much past 40cm unless it's really dark.
2) You can put something reflective that floats in the tank. Then you are ranging off the reflective floats rather than the water. I've seen shiny Mylar beads used. They were too large to get sucked into the outlet, and pretty cheap.
Your other question about the 'glass'. We recommend you use a coverglass in all cases. Polycarbonate or Acrylic works well if you don't want to use actual glass. The trick is to use as thin a material as is practical, to place the sensor VERY close to the cover, and to use a cover that is as flat as possible. Search for VL53L0X coverglass on YouTube.
https://www.youtube.com/watch?v=puRvRsrfpTs
This video will explain a lot.
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