We have had a business for a couple of years and purposefully have not paid ourselves a salary because we had some other income that would create a tax liability but we are concerned that the IRS may begin to question why we have close to $50,000 in our checking account and why we have not paid ourselves a salary. Any thoughts?

What kind of entity is your business? (e.g. sole proprietor, S-corp., LLC?)

We have an LLC

It is already taxable income whether it stayed in your LLC checking account or if you paid it out as salary. In other words, leaving it in your LLC checking account doesn't defer income taxes.