Why is van der Waals radius greater than covalent radius for covalent compounds?
1 Answer
Simply put, because it deals with unbonded atoms.
Explanation:
The van der Waals radius and the covalent radius actually deal with two different situations.
The former is used when dealing with atoms that are not bonded, and the latter is used for atoms that are covalently bonded.
The main reason for why the van der Waals radius is greater than the covalent radius is that it does not take into account overlap.

When two atoms form a covalent bond, their electron clouds overlap. In essence, that is what a covalent bond really is - an overlap between orbitals.
Since a part of their electron clouds overlap, the atoms will be a little closer to each other. This is why, when you measure the internuclear distance between the two and divide it by 2 you get a smaller value.
Here's one more image of how the van der Waals and covalent radii look for the same element

The overlap that exists between the two electron clouds is what causes the covalent radius to be smaller than the van der Waals radius.