Sorry, it was unknowingly.
Sorry, it was unintentionally.
Yes, there is a difference. Unknowingly implies that the person didn't even realise they had done whatever it was. Unintentionally does not have that implication: they might or might not have realised they had done it, but either way they didn't intend to.
Incidentally, neither of those phrases is idiomatic: Sorry, it was unintentional is idiomatic, but the only similar form I can think of with unknowingly would be Sorry, I did it unknowingly, and even that sounds a bit stilted. More natural would be Sorry, I didn't realise (I had done that).