Hi Atomicsirens,
There are several 3rd party eCommerce setups/shopping carts solution that will allow you to set the rates and then collect sales tax automatically, by zip-codes. See Link hidden: Login to view and Link hidden: Login to view
The tax rates also be set manually, and here’s a tutorial on how to set them, by zip codes, at Google Checkout
(see video 1) Link hidden: Login to view
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For a calculator for these rates, you can refer to Link hidden: Login to view
Some create an excel spreadsheet of the zip codes and integrate it into a shopping cart, say Link hidden: Login to view
I completely understand how exasperating it would feel to do business in a tax system as complicated as NY's. :) But be consoled that you're not the only one, in fact even those in the business for years are still struggling with this issue. Let me share with you some discussions, but do not get confused, as a lot of unverified information adds to the mystery. :)
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Let us know if you need further help. :)