If it's cash under the table no taxes then you have to walk out and find somewhere else to work unfortunately. You're both "in the wrong" so it's more of an honor system thing than a court and lawyer thing.
If it's actual missing money on a check and you get a w-2 or file your own taxes that's a crime. As long as there is some way to prove it
then report them and the feds will steal their busi.....er put them in some hot water. If you have no proof then it's ultimatum time and you might end up quitting/getting fired or possibly getting your money and they don't try to pull it on you again.