Then order your FBI and State clearances and find out what's there. Then decide what to do.
Also, rjessome is right that the FBI clearance is supposed to be mailed with the PR application - but it's also possible, if you don't have it back in time, to mail the PR application to CPC-Mississauga to have it assessed with a cover letter telling them that the FBI clearance is still pending. When your application gets to Buffalo, they will write to you and ask that you submit the FBI. They will give you a certain amount of time to submit it directly to them - they won't do any processing on your application in the meantime. Once they receive it, then they will finish their assessment and finalize your application.
Also, I don't agree with chelley's suggestion about the "what if" scenario that somehow they might decide to call an interview and start questioning your wife about something she knows nothing about . . . That won't happen because, if they call an interview, it will be you they interview - not your wife. However, if they refuse the application because they find you criminally inadmissible - for whatever reason, justified or not - she will be notified of the reason for refusal and that could be more detrimental to your relationship than just telling her yourself.
I don't know - certainly don't want to pass judgment . . . but I guess it really has to do with your motivation for keeping it from her, and you're the one who has to live with that. Lots of people do things they're not proud of and, most of the time, that type of history is better left in the past. But it's something else entirely when someone tries to hide something of a very serious nature in order to give themselves an advantage. I can only hope that's not what you're doing.