If you have installed macOS Sierra, you can now use tabbed windows in Cyberduck 5.2 or later. You might want to enable tabs by default when choosing File → New Browser by selecting in System Preferences the checkbox Dock → Prefer tabs when opening documents: Always. New browser windows and the transfer window will then be displayed in a single window frame with a tab bar. You can merge windows with View → Show Tab Bar and Window → Merge all Windows.
Refer also to Use tabs with apps on your Mac.