Honors College or WISE would offer benefits beyond the Honors in the major. Your first two years, you’ll mostly be taking classes outside your major, and by being in the Honors College, you’d be in smaller, more interactive classes.
(Keep in mind that 3/4th of your classes your first year, and 2/3 total, will NOT be in your major, so the best experience you can get both in your major and in your other classes would certainly make a difference).
In short, BOTH would be good, but honors in the major only applies your 3rd and 4th year, whereas Honors or WISE would start right away.
I strongly recommend you email WISE, as the program is supportive and the young women all enthusiastic about the sciences. It’d be a fantastic community for someone who plans on going to graduate school.
Considering the Honors programs, you have a foreign GPA, which may not be all that accurate compared to American GPAs; the fact you scored very high on the SAT, when you took it in a foreign language, should help the Honors committee make a decision. Email them and highlight these two points, as well as your motivation. As Anhydrite said, indicate that being international, you didn’t realize what the programs were or that you were supposed to apply, but ask whether they’d be willing to consider you?