You are getting taken advantage of. Start looking at other companies and DO NOT disclose your current salary during negotiation. Your salary could double and you still might be a bargain in NYC.
When I've worked at start-ups in the industry (I've worked in Palo Alto, SF, Seattle, and other places in NYC), it was like, working crazy hours, constant stress and drama, dealing with annoying requirements, and basically working on stuff I don't care about, like mobile apps, vying for popularity, etc.
If a startup wants to pay me to work on these Astronomy simulations I've made, I'd be interested: https://github.com/ccnmtl/astro-simulations (this is what I've done over the past year at Columbia).
If you are comfortable earning what you earn because of the work you do I get it. I looked into working for research universities in the past like UPenn because I'd be working in say cancer research, etc. I get it.