Married filing jointly is almost always best. Your wife's social security will be partly taxable if your income is more than $32,000 (roughly speaking, it's a bit more complicated but we can ignore that for now). If her social security is taxable and she is not having tax withheld, then you will need to make up that difference by either paying more tax or getting a reduced refund.
However, if you file as married filing separately, your wife's social security income will still be taxable, and both of you will be taxed at a higher rate, and some important tax benefits are reduced or disallowed.
