I didn't think Nassau was horrible. Yes there are definitely some cons mentioned above. However residents were happy, they get plenty of autonomy and all of the faculty I met seemed very friendly. Quite frankly the idea of not having lectures sounds awesome to me... I don't find lecture helpful and usually end up sleeping/dozing through them. They didn't ask me any illegal or trick questions.
I've actually been comparing those two programs and I'm not sure which is a better fit for me either...
Nassau
-pros: medium sized program, front-loaded, plenty if autonomy, residents were happy, 4 9-day weeks of vacation, avg cataract # for ny program, close to the city
-neg: not academic, no funds for supplies/books, 9-wk lecture series in Maine you have to find your own housing for
Stony brook
-pros: lecture series well planned out, funding for books/supplies, residents were happy
-neg: very little autonomy, have to commute to VA which is a 40 min commute 6 mos out of the year, tiny program so frequently on call