Vernon saw the massive horde of thousands of walkers pouring into Savannah at the end of episode 4, so they probably knew that they were screwed. While he may not have liked the idea of a boat, he could probably assume that getting on it would be safer than battling the sea of death all by their lonesome. Their only safe haven was the fallout shelter and it gets swarmed just as well.
Even if he cares for Lee and his group, he knew the size of the boat and would probably choose his people who he may have been with for a very long time compared to a bunch of strangers he just met. Just as well, he had been living in Crawford for a time before fleeing underground, so he also probably knew that there were likely no other boats to be found in the city.
In the words of an awesome fanart, Vernon.....I will find you. I will kill you.
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