My mother-in-law is on my wife and I's checking account. We are applying for her to get medicaid, but not sure how we can get us off of the account.

Since this account belongs to you and your wife, you just need to have the bank remove your mother-in-law as a signer.  If she is a co-owner, you need to close the account and transfer the funds to a new account.  If your mother-in-law is denied eligibility for medicaid because of a transfer of funds related to this account, according to you, you should be able to establish that the account was yours and funded by you from your own funds and that your mother-in-law was shown as an owner only as a matter of convenience.