Spectra, qua representing objects of cohomology theories, are unique up to equivalence (i.e. up to isomorphism in the stable homotopy category $\mathrm{SHC}$; what this means precisely depends on your choice of model).
In fact, there is very little to this argument (and I have to admit I do not understand the confusion in the comments, or the need to cite any literature for this): Let a cohomology theory $E^*\colon \mathrm{hTop}^\mathrm{op} \to \mathrm{grAb}$ be given where $\mathrm{hTop}$ is the homotopy category of spaces (whatever this precisely means to you) and $\mathrm{grAb}$ is the category of ($\mathbb{Z}$-)graded abelian groups. Let $\mathrm{Sp}$ denote your favourite choice for a (model or $\infty$-)category of spectra. The Brown representability theorem spits out a spectrum $E$ such that $E^* \cong [\Sigma^\infty_+ {{-}}, E]$ as functors $\mathrm{hTop}^{\mathrm{op}} \to \mathrm{grAb}$ where $\Sigma^\infty_+\colon \mathrm{Top} \to \mathrm{Sp}$ is the pointed suspension spectrum functor. This extends to a functor $\mathrm{SHC}^\mathrm{op} \to \mathrm{grAb}$ by omitting $\Sigma^\infty_+$, i.e. by sending a spectrum $X$ to $[X, E]$. But this is just a Hom-functor, so the Yoneda lemma yields that $E$ is unique up to isomorphism in $\mathrm{SHC}$, q.e.d.
"But what about phantom maps?" You say that maps between spectra are richer than maps between cohomology theories. This is not true. In fact the proof above shows that there is a bijection between maps $E^* \to F^*$ and maps $E \to F$ on representing spectra up to homotopy since the Yoneda embedding is fully faithful. What is true is that maps between spectra are richer than maps between homology theories. Recall that if $E$ is spectrum, then the $E$-homology of another spectrum $X$ is given by $E_n(X) = [\Sigma^n \mathbb{S}, X \wedge E]$ where $\mathbb{S}$ is the sphere spectrum. This isn't simply a Hom-functor, so the Yoneda argument does not apply, and in fact the functor assigning $E_*$ to $E$ is not faithful. It is however full, and moreover it is still true that the spectrum $E$ giving rise to $E_*$ is unique up to equivalence (i.e. the functor is conservative), for a reference for which and more on phantom maps I will commend you to Lurie's Chromatic Homotopy Theory Notes, Lecture 17.