As a serial collector of flying magazines, I have read most over the years (and still have all the back copies but that is another story.....)
In the Pilot v Flyer debate, I would lean towards Flyer if just going for one. I always found that it had slightly better presentation and there were usually more articles in it that appealed to me - but it is close.
And, as Ian says, the free landing fees can come in handy!
FTN is also worth a look and usually has a few good articles - notably James McBride's column. But this is not a direct competitor to Flyer/Pilot.