Jim, I believe that most of these (perhaps including some CSN vessels) are held at the National Archives. I think I also remember some mention of a few held at the Smithsonian Institute, as well. The NA definitely holds a large number of these (Union vessel plans), but I don't know how many are at the Smithsonian. Perhaps a check of their web site may yield some data on this.
However, it should also be noted that usually not all the plans, for every vessel, are available, and I believe that the plans were usually done up for the original vessel in a class of vessels, and the rest were structured upon the plans of this original (with some minor variations). For instance, I tried to obtain plans, many years ago, for the USS AGAWAM, but was informed that only the plans for the USS SASSACUS were available in that class (the SASSACUS class double enders), so I am assuming that the same modus operandi was followed with all other class of vessels.
I will check a couple of reference volumes I have and see if there is any mention of the CSN vessel plans, and will get back to you if I find any such mention.
I assume you have seen the construction drawings of some of the CSN vessels available online at the Naval Historical Center web site?