At least for the next year, NYC indie productions can take advantage of the NY tax incentive. According to Crain’s, the state has approved another $350 million for film and tv productions. Also for those who are shooting in the city, remember the city gives a 5% incentive.
The links provided take you to the city and state regulations and applications on their respective sites. In addition, the Mayor’s Office of Film, etc. has a page with incentives, which include the Federal incentive for lower budget productions. (Please note: their FAQ doesn’t reflect that the bill was extended for the year.)