So overall you have a really strong profile and I think you can apply freely to the hardest reaches on your list and might get in. I think the fun part will be identifying your favorite likelies and targets–which you might well end up preferring to some more selective colleges.
Animal Sciences near NYC with your other preferences is a kinda interesting combination–that could narrow things a lot. Of course you could do Bio too, and then that superficially doesn’t narrow things much . . . except Bio comes in a lot of flavors, and I think some departments, particularly at smaller colleges, may be more interesting to you than others.
For Animal Sciences, Cornell is an extremely obvious reach academically, but I wonder about your no middle of nowhere preference.
And then I agree about giving Delaware a good look. Sounds like your sort of setting and campus, they have Amtrak, they have an Honors College, they have Animal Science . . . just seems like a solid likely option for you.
For Bio, I didn’t see Haverford on your list. But you just might prefer Bryn Mawr, including because Haverford’s Bio is pretty MCB focused (sometimes known as red biology, and it seems to me maybe you are more a green biology type, with Bryn Mawr doing a lot more of that). Since they are so close, though, you might consider visiting both, indeed if only to get a better sense of how the Bi-Co would look.
I then also agree about looking at both Smith and Mount Holyoke. They both have really well-recognized Bio programs, and Mount Holyoke I would think would be a bit easier admit for you. Both appear to have a lot of “green” and animal-sciencey-stuff in their Bio Departments, and of course they are in Five Colleges too.
As a final thought, have you looked at Rochester? Stretching your distance a bit, but there is a direct Amtrak service. And otherwise, it seems like a fit that for you could be either a likely or at least softer target. I know it isn’t a formal consideration, but they also offer a lot of named merit scholarships, which never hurts. Rochester is a pretty nice city, the university has a nice campus, and they have a very good Bio department. They have lots of tracks within the major, including a “green” track (Ecology and Evolutionary Biology). Again, just a thought for a college that might be an easier admit for you but actually be a really strong fit.