I am in Nassau. My oldest son attended a BOCES Alternative HS in this county and it was wonderful for him. He is slightly Aspie and has some ADD. Unfortunately, it didn't really help him with transition to college - we just found out 2 days ago that he hasn't attended one session of his English 101 at Nassau Community, so college is a no go despite his high IQ.
I don't know that alternative school, but I suggest that you visit it with and without your daughter. Talk to the staff and the other kids. When H and I visited the school my son went to, he almost flipped out seeing the outfits, etc. that the other kids wore. By the time we left, H was ready to adopt the long haired boy wearing thigh high lace up boots, an open vest with no shirt and masses of chains topped off by a spiked dog collar because he was SO polite and bright. After a one hour visit at the school, my son had more friends than he had made in 7 years in district. You will know right away if the school is right for you. My son is straight but the school and the kids were beyond tolerant, sexual orientation was a non-issue.
As for the available programs, I have the same situation in my district. My middle schooler is bussed to Queens every day to attend a private school at district expense because the only options we have are a self-contained (same problem with it that you have) and an inclusion which takes SIX kids per grade (average grade size is about 350). My son is dyslexic, high IQ and can't work fast enough for a regular class in writing, etc.
Yours is a good SD - we actually looked at it, but it's too far out as I work in the city, but most districts don't get that kids can be bright and have Learning Disability (LD)'s too. Most don't get Central Auditory Processing Disorder (CAPD) at all.
Last word of advice, get a full IEP as it will protect you more than a 504. Also, my son's BOCES school did not take kids without IEPs, check on the alternative school's rules.
Good luck.