I think you're right, BofB. The novel calls it "The Five Families War of 1946." But since Stracci and Cuneo weren't killed, the most likely reason that Michael didn't move against them is that they didn't side with Barzini and Tattaglia during the war--or at least didn't take an active role in the fighting. And, yes, the novel does say that they weren't physically located in the Five Boroughs of New York, so territory might have been a factor. The film, of course, had all of them inside the borders of NYC.
Geography wasn't a factor in real life. In the famous Castellemmarese War of 1930-31, Capone (Chicago) helped Masseria (Brooklyn), while Magaddino (Buffalo) helped Maranzano (Brooklyn). Other out-of-towners also pitched in.