Assume you are given a non-negative, continuous, radial function $f\in L^q(\mathbb{R}^3)$ (for any $q\geq 1$).
Are there any conditions which would guarantee that the Fourier transform of $f$, that is $\hat{f}(p)$, is also non-negative?
the three-dimensional Fourier transform $F(\vec{p})$, of the radial function $f(r)$ has Fourier transform
$$F(\vec{p})=\int_0^\infty dr\int_0^\pi d\theta \int_0^{2\pi}d\phi\;e^{ ipr\cos\theta}f(r) r^2\sin\theta$$ $$\qquad=\frac{4\pi}{p}\int_0^\infty rf(r)\sin(pr)\,dr,\;\;{\rm with}\;\;p=|\vec{p}|.$$
so you're asking when the Fourier-sine-transform $S(p)$ of $rf(r)$ will be (pointwise) positive for $p>0$. A sufficient condition is that $rf(r)$ is a decreasing function of $r>0$, see On positivity of Fourier transforms.
For a related question, see this MO post.
For the connection to Bochner's theorem: the OP's question amounts to finding a function that is both positive and positive-definite, since positive functions have positive-definite Fourier transforms.
The magic words are "Bochner's theorem" (which says that the Fourier transform is positive for positive definite functions). For more on radial functions see Theorem 2.4.1 in this book. (Greg Fasshauer)