In this work, we present new data on the $^{89}$Y($gamma$,n) cross section studied with a quasi-monochromatic photon beam produced at the NewSUBARU synchrotron radiation facility in Japan contributing torwards resolving a long standing discrepancy between existing measurements of this cross section. Results for $gamma$-ray strength function below threshold obtained by applying the Oslo method to $^{89}$Y($p,pgamma$)$^{89}$Y coincidences combined with the $^{89}$Y($gamma$,n) data this providing experimental data for the $gamma$-ray strength function of $^{89}$Y for $gamma$ energies in the range of $approx 1.6$ Mev to $approx$ 20 MeV. A low-energy enhancement is seen for $gamma$-rays below $approx 2.5$ MeV. Shell-model calculations indicate that this feature is caused by strong, low-energy $M1$ transitions at high excitation energies. The nuclear level density and $gamma$-ray strength function have been extracted from $^{89}$Y($d,p gamma$)$^{90}$Y coincidences using the Oslo method. Using the ($gamma,n$) and ($d,pgamma$) data as experimental constraints, we have calculated the $^{89}$Y($n,gamma$)$^{90}$Y cross section with the TALYS reaction code. Our results have been compared with directly measured (n,$gamma$) cross sections and evaluations. The $N=50$ isotope $^{89}$Y is an important bottleneck in the s-process and the magnitude of the $^{89}$Y(n,$gamma)$ cross section is key to understanding how s-process stars produce heavy isotopes.