It sounds like you have quite a decision to make! I can't tell you what the right answer is, but if I were in your position, I would probably go with School #1. It all depends on what your priorities are, but it sounds to me like you prioritize family and loved ones over your academics (and I absolutely do not judge you for that -- I am the exact same way, which is the reason I applied exclusively to programs near my family). And if your relationship with your boyfriend is very serious, I wouldn't jeopardize it with the strain of going to School #3 - as wonderful as the program may be, long-distance is never easy. As for School #2 in NYC, I'm about to say something really unpopular: as someone who currently lives here in NYC, I do not recommend it. If you grew up in a place where there's clean air, quiet, and enough space to walk down the street without getting head lice from the nearest person on the sidewalk, you might not like it here. I mean, there definitely are great things about it (i.e. you don't need a car at all, ever, which saves a lot of money) but it's a very stressful place to live. It all depends on your personality -- a lot of people really thrive in a bustling atmosphere like NYC, and they love that it's always so busy and vibrant here. Personally, I prefer a city like Boston. But that's just me. If you haven't visited New York before, it's worth coming down to see if you think it might be a good fit for you.
It sounds like School #1 is a nice place, relatively affordable, close to the important people in your life, and will provide you with a clear (and quick) path towards your ultimate goal of doctoral study. It sounds to me like School #1 satisfies both the head and the heart.
Those are my thoughts, anyway. Good luck with your decision!