I am a big believer in bootstrapping and DIY, especially when it comes to starting a business. One, you don't have much money to waste, and two, knowledge is power.  Thus, before you pay some incorporation service to essentially operate a fax machine for you, you may as well do it yourself all the way and learn a lot by doing it.  While you could hire a lawyer to do it for a ridiculous amount of money, it really isn't brain surgery, at least not when you are a one man/woman business just starting out.

Searching the internet for good resources to do so, I came across the Do-it-yourself Kits offered by Stephen L. Nelson, a CPA in Redmond, WA.  I reviewed the "New York S Corporation Kit" and the "Setting S Corporation Salaries" ebook.  I found both publications extremely informative and helpful.  They have everything you need to know to get your New York s corporation on the road.  He charges a modest amount for these publications, but also offers tons of helpful free information on his website. 

Nelson is also the author of the bestselling book series, Quickbooks for Dummies.  Another startup resource that I highly recommend.  A working knowledge of bookkeeping and accounting principles is a must for every new or aspiring business owner.   My favorite title is "QuickBooks 2010 All-in-One For Dummies."

By the way, I don't personally know Stephen L. Nelson or have any incentive in endorsing his products.