Check out the port list at Ikelite's website. Looks like neither would work with the 5503 dome port, so you'd need another port, in which case I'd look at getting a flat port.
Both are fixed focal length lenses. The 50mm is a little more versatile in that you can get 1:2 without the lifesize convertor (1:1 with) but still take reasonable "fish portraits" from a reasonable distance.
The 100mm is a native 1:1 lens and due to the longer focal length is a bit trickier to use. It gives you more working distance which is great for small, skittish subjects, but not so great for larger subjects.
If you want to cover more focal lengths, getting the 100mm makes more sense because you technically have 50mm covered with the kit lens. If you want a more versatile lens, the 50mm makes more sense. If you do go the 50mm route, you might want to look at the Sigma 50mm, which does 1:1 without any convertor, although it is supposedly slightly less sharp than the Canon version.