Both are fine. You could say, "I haven't seen him FOR years," as well. If you want to go to the future... then you need 'for.' ('in' doesn't work). I won't/mightn't/shan't see him for years. However, word it differently and 'in' works: I'll see him in a few years. But for the present and past: I haven't seen him in/for years, I hadn't seen him in/for years. Also, I didn't see him for years. I think it sounds odd to use 'in' here. With 'didn't' - but perhaps that's just me!

I'm guessing that you're asking about changing a sentence from direct to indirect speech. What you have written is correct. The phrase 'in years' doesn't change when you put the sentence into indirect speech.

Both are correct.