Ok but here's a random thought,
McGonagall knew about James' animagus form because it didn't take too long for her to see a connection between the stag that sometimes just appeared on school grounds ( I mean cmon u can't hide a freaking stag from MINERVA MCGONAGALL) and the fact that every time she gave James detention, Sirius would dramatically exclaim, " oh DEER looks like you're in trouble again"....