What are the laws and procedures for incorporating a 501(c)3 in the state of NY

The answer depends on which corporation is going to be the 501(c)(3). Non-profit status follows the particular corporation. Thus, the answer may be as simple as using the corporation date for the corporation you want to have charitable status. My answer, however, could change depending on the documentation involved.

It also sounds as though you need to "clean-up" these corporations. You would want to consider why you have two corporations and whether they serve your needs. I would suggest being very careful in this matter, however, since you have to satisfy several levels of supervisions since charitable organizations must report to the Attorney General and the IRS. Also, you want to ensure you have been careful in your application to the IRS that you have been clear whether you are being a public charity and a private foundation.