My latest favorite place in New York City is ABC Kitchen which is a farm to table restaurant just outside of Union Square. Great seasonal produce that is cooked to order makes it an ideal style of restaurant for people who have restrictions.
The park slope food coop is also an excellent. place to shop to find alternatives to fit your dietary needs, but it is a commitment as you need to work there to shop! I have been a member for over 7 years and I love it.