How much of the Earth's crust contains groundwater?

This is a good question but very hard to answer.

"Groundwater" is a bit of an irrelevant term. Fresh water is generally restricted to less than maybe 1000 feet but it varies from place to place. All groundwater generally gets saltier with depth. Where I live in the Western Canadian Sedimentary Basin, a typical profile would look something like this:

0-1000 feet = <300 ppm NaCl

1000-2000 feet = 300-10,000 ppm

2000-5000 feet = 10,000-40,000 ppm

5000-10,000 feet = 40,000-100,000 ppm

10,000 - 13,000 feet = 100,000- 250,000 ppm

Groundwater is restricted to the sedimentary basins that have porous and permeable rock, In Canada this would be restricted to about 25% of the country's landmass. If the world is roughly 29% Land and this ratio applied (25%) uniformly (and it doesn't) then only about 7% of the world is capable of storing groundwater and only about 10% of that (1000 feet) would contain Fresh Water. Now you only have 0.7% of the Earth which contains fresh water. Of that 0.7% maybe only 30% of that geologic section would contain porous and permeable rock which is capable of being a fresh water reservoir. So in the final analysis only about 0.2% of the Earth or maybe 0.7% of the landmass can have useable fresh water resources. This is a very very rough estimate on my part. An additional calculation that would have to be applied is the average pre space of the reservoirs within that 1000 foot window (maybe average 35% porosity) which further reduces the amount of water down to between 0.24%(land only) and 0.07% (entire Earh Surface).

This is a 10 minute estimate. To do this properly would take about 1 month of solid work and it would still be a very rough estimate.