'Stephen Culp (I)' plays Commander William Skinner. The same actor played the recurring character of CIA Agent / Deputy Director Clayton Webb on JAG (1995), the show on which NCIS originated in Season 8.
The Chimera ship is in fact SS Lane Victory. When Gibbs and Dr. Mallard first go inside the ship you can see near the door a sign with "KECW". That's an alias for the ship SS Lane Victory. They even show a picture with the ship having additional lights for this episode, on their site lanevictory.org. The same ship was used to film scenes from Flags of our Fathers (2006).
The nature of the USNS Chimera bears a strong resemblance to the real life USNS Glomar Explorer (http://en.wikipedia.org/wiki/Glomar_Explorer). Both ships were operating under the cover of a civilian ship, and both ships true missions were the covert retrieval of Soviet/Russian nuclear weapons on the ocean floor.