Of the schools you listed, here’s my opinion for a “chance me.” Again, this is only my opinion and others will certainly disagree.
Columbia: I don’t think this school is going to happen, even if you try to fix those core deficiencies within the next year before you apply. Columbia has a prerequisite chemistry course that students take freshman year, and the fact that you haven’t had AP Chem, or an equivalent higher level course in chem, will certainly come up in discussions about your file and hurt you most likely.
Barnard: This is a better fit, but again, with some of your core deficiencies, this is probably going to be a bit of a stretch for you to get in next year.
Colby: Ditto my comment for Barnard with this one.
Bryn Mawr: I think you could get admitted here if you write the heck out of the application and find a way to discuss your Hispanic background in the essays. While all these schools look for URM, Bryn Mawr could really use more of them, so I’d use that to my advantage.
Middlebury: They aren’t going to like that language deficiency stuff, methinks. Unless you fix some of that by taking an outside language course online (for a grade) or at a local community college over the summer, this could be problematic with getting in here.
Ithaca College: I think you won’t have a problem getting in here.
CUNY JJ: I think you will be competitive for this program with the stats you’ve mentioned.
The main issue for your reaches will be your lack of some core stem areas when you are intending to pursue an environmental science field. Even if you haven’t been able to take them through your school or whatever, admissions will still ask about your readiness. It will be brought up and discussed.
If you can’t find a way to fix some of those existing deficiencies outside your school by the time you apply, I’d suggest also looking at places outside the NE area too. I mentioned William and Mary, but I’d also look at Tulane.