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If your business is a registered legal entity (e.g. Corporation, LLC, or Partnership), then you would have to retain an attorney in order to represent the business in court, including small claims court.
This is because a legal entity is considered a separate "person" from it's owners and only a licensed attorney can represent another party.
Having said that, sometimes business owners do represent their entities in court. Unless the defendant objects, the court often will not raise the issue itself.
So, it's possible to get away with it, though it is not technically allowed.
As for where to sue, you can sue where the contract was formed.
However, you should revised your contract to include a venue provision that states that such and such court or county will have jurisdiction and venue over disputes.
That will avoid any dispute over where you file in the future where you get a defendant that tries everything to avoid your suit.
Here is a link to a guide for using the small claims court in NY:
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