i can't comment on JFK, since I've never been there. But, I have heard many horror stories about that airport. So, you might be well advised to stay away from it. I have.
As for LGA, there are a few places.
First, is the west end of the USAirways terminal (which is shaped sort of like a horse shoe). There are a couple of windows there that allow some great taxi shots-even when the gate that's there is occupied.
The next, is in the Central Terminal. There is a walkway between the concourses that has lots of windows tht overlook the tarmac. The only drawback to this is that you can only get good pix of planes arriving or departing the gates that you happen to be overlooking.
The next best is at the end of the C concourse, where United is. When those gates aren't occupied, that is (in my humble opinion) the BEST spot at LGA. The main drawback to this spot is simply getting to it. It is restricted to ticketed passengers only, so you may have to get a gate pass from one of the airlines (I found that if you cry and plead, TWA will usually be the one airline to give you one).
Almost as good as concourse C is "D", where American parks. SImilar view as C, but a better view of the runways. Also, taxiing planes pass much, MUCH closer to you. This is also a "ticketed pax only" concourse, but it's not as rigidly enforced as the others, so it's possible to sometimes "sneak in" without bearing a ticket (be sure to pass through the metal detectors though). If you do get in, plan on staying awhile (you won't be disappointed) because if you try it again later, you might not be so lucky..especially if someone happens to notice the same person passing through security over and over...good luck