You should contact the NYS Dept of Labor about not being paid. They will try to get the money for you. My experience is that small cleaning companies are hard to sue. They disappear easily and usually hard to locate.
The EEOC has stated that it considers it to be discriminatory for an employer to base an adverse change in working conditions, including termintation, on an arrest, if the person is a minority employee. Contact the union asap.
It sounds like you are the one asking to be paid on the books, and your boss is refusing. So, I do not think that will be a problem for you if you decide to sue. It will be a problem for the company. Also, you are probably entitled to unemployment benefits if you quit, even if you are off the books. In any event, you should consult an attorney to discuss your rights and options before you decide what to do.
Most employees who work off the books are not paid properly and can sue for violations of minimum wage laws or unpaid overtime. Also, many bosses will agree to severance pay when there is a possibility of illegal transactions being disclosed. You can consult an employment lawyer to discuss your situation.
It does not amount to discrimination until he implies that unless you return his advances you will not be hired. If he follows up by email, you should print out a copy of the communications. If he calls, try to record the conversation. Any hint of him giving you a good recommendation to his boss if you respond favorably to his advances, or that he will give a bad one if you don't, will constitute grounds for a law suit.
In my opinion, no, because once the time for an ACD (Adjournment in Contemplation of Dismissal) to be finished has passed (usually 6 months) you should no longer have to disclose it since the charges are now dismissed.