Ever since the 5th season it has become a standard procedure for Family Guy to release extended versions of the episodes on DVD. Therefore it's no surprise that the DVD Version of the two-part episode Blue Harvest is 4 minutes longer than the TV Version.
Similar to the 3-episode series Imaginationland from the series South Park, the producers decided to leave the episode out of the respective season-box-set and instead released Blue Harvest on a separate DVD. Not all the extensions are that important (you wouldn't really miss most of them in the TV Version). All in all, the DVD Version still seems to be run a little smoother, especially because Joe, Tom Tucker, Diane Simmons and Ollie Williams can only be seen in the DVD Version. Also, the black dolphins only in the DVD Version do what they're known for.