While I cannot provide a definitve answer for immediate help - I can tell you, as a former subcontractor in the trades - you need to see an attorney in your area with experience in contract/construction issues before your guy goes south and disappears.
You've already got all of the signs of a failing business - and 3 to 4 months is too long to float him your $25k loan.
Contractors in Nassau County are governed by the Nassau County Department of Consumer Affairs. I urge you to immediately contact and file a complaint. They may also give you some additional information as to what your rights are. You may also want to consider retaining an attorney to bring suit (Consider calling the Nassau County Bar Association for a referral), or you can bring a small claims action yourself in Nassau County District Court. Good luck!
This is unfortunately a growing problem on Long Island. While a detailed review of the specific facts of in your situation would be needed for a complete and thorough answer, the short answer is that even if he is incorporated, he is not completely protected under NY law. Since you indicated that you have paid him but not received services, it is possible that he could be in violation of NY's statutory "trust" created under the Lien Law. If he is found to have violated the trust, he is personally liable regardless of the corporate form. Your best bet here is to contact a construction attorney right away.
I agree with the answer given by the last attorney who said that in Nassau County the Consumer Affairs Bureau is the way to go. You can find them on Google or in the phone book. If you register a complaint with them, they'll call the contractor in and usually give him a direction to complete the job or they'll take action. It also may turn into a criminal complaint if he's taken two deposits from you and not finished the work.
As for your concern about him being incorporated and going Bankrupt, he may also be personally liable under the criminal law if he's used up your deposit without finishing the job. I strongly suggest you get yourself a lawyer and proceed immediately, regardless of the potential for Bankruptcy.