Former New York entrepreneur here. There's a simple solution to this: don't incorporate in New York. You can incorporate in any state you want simply by having someone to receive your mail there (known as a "registered agent").
The laws in New York are absurd. I incorporate in Florida now, and it costs $70 and takes filling out a 5 minute form.
If you physically operate out of New York, that does still require paying NY State a $300/year "foreign corporation doing business in New York" fee, plus a one-time $225 filing fee: http://www.tax.ny.gov/pdf/publications/corporation/pub24.pdf
The laws in New York are absurd. I incorporate in Florida now, and it costs $70 and takes filling out a 5 minute form.