I just got back last week from a vacation in which I spent 10 days on Culebra and four on Vieques. I'm an avid snorkeler (don't scuba anymore), so I might not be able to give all the first hand info you might need as a diver. However, I did a lot of research regarding both islands before I went, and I also spent many hours snorkeling there at various locations, especially on Culebra. My impression is that Culebra is considered the better diving spot, especially because the water is usually clearer than in Vieques. My snorkeling observations support this generalization. The vis for beach snorkeling in Culebra was usually about 30-40 ft (absolute max of maybe 50 ft on a couple of occasions in limited areas), whereas it was only 20-25 ft in Vieques. I mentioned this limited vis to the guy in the dive shop in Vieques, and he said that because of the persistent winds while I was there, they weren't getting much better vis on the offshore scuba sites, either.
Other observations: Although there was very good growth of coral on Culebra, it was the most non-fishy place I have seen in the Caribbean (I've been to the Bahamas, Grand Cayman, Cozumel, Roatan, and Akumal). There were very few fish other than the typical small/juvenile wrasse, grunts, and damsels you see everywhere in the Caribbean. I wonder if this is also true at scuba depths. I saw more pillar coral in Culebra than I have seen elsewhere. There is one dive shop on Culebra that runs dive charters (Culebra Divers), and I think there is someone named Taz or Traz that also takes out divers. The main dive operation on Vieques is Blackbeard's, which also has a dive shop. I really enjoyed both islands. They didn't have mega-tourism and cruise ships, thank God. They are quite different from each other and each has some advantages. Before I went, I thought I would like Culebra much more, and I was surprised to find that Vieques was better than I expected. Bottom line - I don't think either island can be considered a "world-class" dive destination such as Cozumel or Cayman, but I think you could have a very relaxed and fun dive vacation there.
If you want more info, send me a p.m.