NPM was Pearl Harbor. I think (but am far from certain) that NPY did not come into service until after the war. In every first-person narrative by submariners I've come across they mention guarding the NPM frequency and I've never read anything about NPY. Here are a few others used by subs during the war:
NPG = San Francisco
NPN = Guam
NPO = Cavite
NPR = Dutch Harbor
NKN = NAVGROUP China
VHM = Brisbane
VHF = Fremantle
Not sure if you've found this site before but it is fascinating and detailed reading about submarine communications procedures and the Fox schedules:
http://www.ka8vit.com/subops/subop5.htm