Have you contacted the Intrepid Sea-air-space museum? They're located at pier
86 (I think at 42nd street and 12 Ave.) in New York City. Next to the
aircraft carrier they have a one of the first generation missile/drone
launching subs (not a nuclear-powered one, though). For many years, the museum
had serious funding and maintenance problems (drug deals, etc...) but they seem
to be back on track. They are definitely more oriented towards being a public
attraction than towards conserving the artifact, but who knows, that may have
changed, too, and they may have some advice on how to proceed.