The underlying reason why we use $\cos$ for $x$ axis, and $\sin$ for $y$ axis, comes from Euler, and complex numbers in particular: $$\begin{align} z &= r e^{i\varphi} \\ \vec{p} &= \left ( r \cos\varphi, r \sin\varphi \right ) = \left ( \operatorname{Re} z, \operatorname{Im} z \right ) \end{align}$$

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So, if you want to consider clockwise angles positive, just use a left-handed coordinate system (where $x$ increases right, and $y$ downwards).

Positive angles are counterclockwise only in right-handed coordinate systems, where $y$ axis increases upwards, and $x$ axis right.

In a left-handed coordinate system, $y$ axis increases down, and $x$ axis right, and positive angles are indeed clockwise. Such coordinate systems are often used in e.g. computer graphics.

A rather peculiar question and off topic in every way but though. In almost every situation clockwise is considered to be positive but not when it comes to angles. Why is that? Euler's fault or ...

(Note that by rotating the coordinate system 180°, $x$ axis increases left, and $y$ down; I do not recall seeing this convention anywhere in practice, but I guess it would be just as natural to predominantly left-handed people. It is just that most humans are predominantly right-handed, and that does seem to permeate our culture in very subtle ways.)

One reason: this way, angles between $0$ and $\dfrac \pi 2$ are all in quadrant $I$, so that the sides of right triangles in a quadrant with positive coordinates have positive lengths.

Do remember to state your preferred handedness, though; most mathematicians et cetera assume a right-handed coordinate system unless stated otherwise.

If you want a justification for such convention, I think that it is physical. In a Cartesian plane we usually identify the $x$ axis as horizontal and the $y$ axis as vertical referring to our world where the direction of the gravity is orthogonal (and vertical), with respect to the horizon. And we assign the positive direction of the $x$ axis from left to right and the the positive direction of the $y$ axis from down to up. So it is more simple to assign the positive direction to an angle if it rotate the positive $x$ semi-axis toward the positive $y$ semi-axis and this is the counter clockwise direction.