Have you applied anywhere yet? Have you visited these places?
- Your first limiting factor is where you get in. I'd apply to all of the schools you're interested in and see. If you don't get in to either of the schools in NYC, the decision is made for you. And vice versa. If you get in everywhere, see what they'll give you. Play them off of each other. Every school wants to attract a prestigous student body, and if they think that's you, they will pay you to be there.
- If you can afford it, I'd visit both places if you haven't already. It's one thing to read about a place and look at pictures, and another to actually be there. I thought I would love LA before I visited, just based on everything I saw online. Turns out, not so much. Sometimes you just vibe really well in a place. It's not something you'd know until you're there.
Both of those cities are great for transfolks. Along with SF, I'd put them in the top 3 "best" places for us to live. So I'd void out any concerns about one being better than the other for trans-specific reasons. California may be more vegan friendly, but I doubt there's a shortage of vegans in NYC.
I know there are some locals here from both of those places. Hopefully they can chime in with specifics that might help you. I'd still say the most important thing is where you get in, and if you could see yourself going there.
