According to the dictionary the two words are synonymous to each other but I think there is a subtle difference in meaning between the two words that I do not find in the dictionary.
I thought of this question when I heard the word 'insinuendo' in a movie. The actor blended the words 'innuendo' and 'insinuation' and created an interesting and funny portmanteau.
Best Answer
"The difference lies at whom the comment is directed and who determines the allegation is unwanted."
While technically the words are considered synonyms of sorts, pragmatics suggest a substantial difference in several aspects.
Bruce Fraser writes in Perspectives on Semantics: