Great film. Who was the Womans son at the end? Noodles from the rape or Max?

If you mean David - who was the spitting image of Max - then he was clearly Max's son. If his uncanny resemblance to traitor Max didn't give it away (it’s the same actor after all), Deborah even tells Noodles that he is Secretary Bailey's (AKA Max) kid. Although I don't think it's made clear whether Deborah also happens to be his mother or not.
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This was 35 years later so couldn't possibly noodles from the time he raped her and seeing as it was the same actor playing Max and David then it was clearly Maxs son.

It was Max's son. Deborah wasn't his mother, just Max's lover.