If I had to choose between just those two I would go with Victoria House. It is at the south end of the island, but much closer to to town. You don't have to get a water taxi to get to town.
There are a lot of good dive shops in AC, so having one right at the resort is just an extra. (Both VH and JE have shops on site) All will pick you waterfront whereever you stay. Once you have been to AC and gotten used to what it is all about you'll see how easy it all is no matter where you stay. The only important thing is not to overpay, not to underdrink, eat the fish you catch, and have a great time.