Is Cy5 hydrophobic?

Yes, Cy5 is strongly hydrophobic.

Cy5 is a commonly used far-red fluorophore. It fluoresces at ~650 nm excitation and ~670 nm emission and is used in a wide range of applications including flow cytometry, nucleic acid labeling, immune-labeling, and fluorescence microscopy.

Cy5 dye is mostly available as a sulfonated derivative for the purpose of increasing its hydrophilicity. The sulfonated derivative, known as Sulfo-Cyanine5, is water soluble for the red part of the spectrum.