Dear steve,
Unfortunately, according to the New York state Department of Taxation, the time of purchase does not really matter. Interestingly, for boats and cars, it is driven by the registration process. In order to register a boat (and vehicles also) for the first time in the state, you have to show that (a) it was coast guard documented, and (b) that you paid sales tax.
It would make a difference if you had paid sales tax in CT.
There is a general statute of limitations on the collection of sales and use taxes of 3 years. The state has three years in which to assess the tax. What I am not able to tell you, is if they actually met this requirement. Generally, in most states, the tax is procedurally assessed at the time of registration. If you claimed an exemption you were not entitled to (even though you thought you were), then the statute of limitations, in many states, does not start until discovery of the fact. We do not know when they discovered the oversight.
let me share this with you. I noticed that several people had filed an appeal with the state based on their individual circumstances. about 2/3's were successful with the appeal or had the tax and penalties reduced.
I recommend that you find a local tax attorney. Sit down with him or her for a few minutes. Nothing beats sitting down face to face with an attorney for 30 to 45 minutes and having a discussion. You may discover a little factoid in your circumstances that allows you to file an appeal. At the very least, your attorney may be able to negotiate for you and get a reduce payment. I am assuming the tax bill will be a couple of thousand dollars and the attorney's fee will be worth it.
If you can challenge this tax based on a procedural issue, then you might be able to avoid it.
YOUR PAYMENT AND BONUS IF ANY MAY BE TAX DEDUCTIBLE

Edward M. Johnson