I would hesitate to submit the 690 Physics score since that is around the 50-55th percentile for that subject test (notice a perfect 800 is only the 90th percentile meaning 10% of students nationally get a perfect score on that test): http://media.collegeboard.com/digitalServices/pdf/research/SAT-Subject-Tests-Percentile-Ranks-2012.pdf
I would instead let your SAT I and Math IIC scores speak to those general skills and not let the subject tests negate/reduce them, especially since you are applying as a science major to the some of the most competitive science magnet schools in the nation. The 3 in AP Physics suggests you may have been nervous (especially if you got an “A” in the course), but the 690 in Physics confirms you probably don’t know the material that well or struggled, which is a red flag for a science applicant where physics is the basis of applied math, a staple of science. Schools like Princeton, Stanford, JHU will undoubtedly be receiving many of those 10% of students nationwide who got perfect scores, and your 690 is going to probably fall 1 to 2 SD below the average subject score in Physics for their applicants (or any science subject test score submitted for that matter). As you said, you are a science major and not an engineer, so this may not be all that important, unfortunately you didn’t take other advanced science coursework or science subject tests, so all that can be referenced by the admission’s committee is your performance in physics (and any grades in non-AP science coursework). If your grades in science coursework are strong then I would definitely omit the Physics subject test and let your grades speak to your science ability. Be wary of offering a direct comparison between yourself and other applicants when you don’t need to, especially in a comparison you will probably lose. Make the committee assume on your other merits that if you had taken the physics subject test you probably would have at least scored their applicants’ mean (which your other scores are meeting or exceeding), instead of proving that you didn’t.