遅いんじゃない？
お遅くないんだ？

Just wondering what the difference between the two is. Do both of them translate to "Are you not late?"

Thank you!

Yes, but with different tones of voice?
It might be better to say,
遅いんじゃない is "You're late, aren't you." (Although I suppose it's possible that in some context this actually means 'Not late', but I find that context hard to imagine.)
遅くないんだ is "You're not late." - This one's unambiguous.

(Of course, the subject could be 'I' or 'John' or whatever depending on context, 'you' is not explicit or even most likely.)

Oh, I dropped the question marks too... the second can't be a question ending in だ like that. The first can be either questioning or not - it's essentially a rhetorical question.