Should I fly out to apply for a new visa or cancel my current visa before leaving Thailand?

Yes, you need to cancel your and your wife's extensions. It had to be canceled as of 12 Oct, so anytime after that, you may or may not need to pay for an 'overstay' fine until the day you apply for cancellation after your extension was invalidated (by canceling your work permit).

You can go to apply for your new visa as planned, then go to the immigration office to cancel your old one as soon as you return to Thailand.

Or you can apply for cancellation on Monday before you leave.

If you leave tomorrow, just be sure you don't have a re-entry permit, or don't use a re-entry permit when you enter Thailand.