However after a little bit of digging I've discovered the solution to this!
By default the package sni-qt is installed with the Skype package by default if you download it from the Ubuntu repository, however if like me you installed Skype by downloading the deb directly from the site, it will not be included.
Therefore quite simply you neeed to install the sni-qt package via terminal:
sudo apt-get install sni-qt sni-qt:i386
In addition to this you may need to add Skype to the Unity notification area whitelist. With the following command you can output a list of the current entries for whitelist:
gsettings get com.canonical.Unity.Panel systray-whitelist
Then use the following to set the array with the addition of Skype:
gsettings set com.canonical.Unity.Panel systray-whitelist "[ ..., 'Skype']"