In order to begin and complete the Bounty Hunter missions, you must have accomplished the following:
Completed Story Mode (for all available bounties)
Completed the "Hostage Crisis" mission aboard the Invisible Hand (to unlock Bounty Hunter missions)
The Bounty Hunter missions can be located on the Invisible Hand.
To get there, simply take the same path you would have taken to get to the "Hostage Crisis" mission. Go up to the platform in front of the curtain to begin. Thanks to jagiber85, an awesome Bounty Hunter mission guide can be found here.