It's a no-win situation for both of you, especially you. But no point bitching. Try to make peace and leave in good terms. Afterall, in the event that he reported you to DHS, you might be barred from entering the US upon your arrival at POE and in that instance, nobody's going to go after him for hiring you illegally. 

I know it doesn't sound fair but that's life. You worked for him illegally because you were in a desperate situation. If this situation called for mere justice, I'd have urged you to try confronting him but you're set to lose more than gain. You'll earn 50 times more in the long run. Let the prick have his way for now. It's just a thousand bucks - that's like what? 2 weeks paycheck? Not a small sum by any means but the consequences might be far more devastating. 

Good luck!