Hi, if I've understood your description and the schematic correctly, and with the little I know, I'd go with the NPN set-up. However, as you say the modem will be mostly on, that's perhaps the most wasteful option, as one would think the PNP would use less power, because it'll be "off" whenever the modem's on.
I have a doubt about that PNP set-up, as in my naivety I'd have thought the microcontroller were intended to supply the positive voltage to the transistor, which I don't understand how it does that if it's configured as an input, but that's my lack of experience with microcontrollers.
I hope a better-informed person answers this for you as my theory may be wrong.
It's an open collector input pin on the microcontroller (isn't it?). Memory's failing me it seems. I think the PNP is the better choice.