In your case, AP Bio might actually look better to colleges since it seems like you don’t have many. Are you sure physics honors is harder than AP Bio? The class itself might be easy, but the AP exam isn’t exactly a walk in the park (if you don’t have a good teacher).
It really depends on what you want to go into. For what it’s worth, physics as a subject is much more valuable in high school since you’ll use it in any STEM career you go into (if you do it right… don’t plug and chug).