We study conditions that ensure uniqueness theorems of Cuntz-Krieger type for relative Cuntz-Pimsner algebras $\mathcal{O}(J,X)$ associated to a $C^*$-correspondence $X$ over a $C^*$-algebra $A$. We give general sufficient conditions phrased in terms of a multivalued map $\widehat{X}$ acting on the spectrum $\widehat{A}$ of $A$. When $X(J)$ is of Type I we construct a directed graph dual to $X$ and prove a uniqueness theorem using this graph. When $X(J)$ is liminal, we show that topological freeness of this graph is equivalent to the uniqueness property for $\mathcal{O}(J,X)$, as well as to an algebraic condition, which we call $J$-acyclicity of $X$. As an application we improve the Fowler-Raeburn uniqueness theorem for the Toeplitz algebra $\mathcal{T}_X$. We give new simplicity criteria for $\mathcal{O}_X$. We generalize and enhance uniqueness results for relative quiver $C^*$-algebras of Muhly and Tomforde. We also discuss applications to crossed products by endomorphisms.