I don't know too much about the stations along the BNSF corridor, but what I can suggest is that you pick one that gets bypassed by express trains, so you can see some stop and some go flying by (www.metrarail.com
has the all the schedules and route maps). The BNSF is loaded with Metra, Amtrak, and freight trains so it's unlikely you'll leave dissapointed, no matter where you watch from.
And officially, there is no rule against taking pictures, unless the photographer is doing something dangerous. However, cops have been known to periodically shoo railfans off because of terrorism fears. This seems to happen more at the downtown terminals than at the suburban stations, and I tend to think the people along the BNSF line are probably somewhat used to the railfans being there, so you shouldn't have much trouble. If you do get hassled, remind whoever's doing it that taking pictures are within your freedoms. More often than not, the officer, not the railfan, has been proven in the wrong in these types of situations.