They're not an NPT thread because it is not the threads that do the sealing; it is the 45-degree flare that does the sealing. Regardless, when I removed my A.I.R. (Air Injection Reactor) tubes, I used BRASS pipe plugs (common hex head that you can find at auto parts stores, hardware stores, plumbing supply places, etc.). I believe mine used 1/4 inch NPT.
Example:
The reason I used brass plugs is that they will thread in a turn or two, and when you put a socket on them and tighten them down another turn or so, the soft brass will deform and do a good job of plugging the hole in the cast iron manifold, and will not leak.
NOTE: you will have to completely remove the existing leaking tube and tube nut for this to work. If you can't remove the remnants from the previous owner's "modification," I'm not sure what will work, other than maybe welding/brazing the ends of the tubes better than what the other guy did.