Because you are the sole owner of the S-Corp, you generally cannot simply present yourself to the mortgage lender as an ordinary W-2 employee and ignore your ownership. Under conventional mortgage guidelines, someone owning 25% or more of a business is considered self-employed.
That means the lender will normally look beyond your pay stubs and W-2. Depending on the loan and your history, underwriting may review your personal returns, S-Corp return (Form 1120-S), K-1, W-2, and potentially current business financial information. The purpose is to determine whether the business—and therefore the income it pays you—is stable and likely to continue.
Your W-2 wages can count, but your S-Corp income can matter too. Fannie Mae permits consideration of a shareholder's proportionate business income when the lender can establish that the income is available to the borrower, either through distributions or sufficient business liquidity. Freddie Mac similarly allows qualifying income based on W-2 wages and, where requirements are met, the borrower's proportionate S-Corp income. Cash distributions themselves aren't necessarily treated dollar-for-dollar as additional qualifying income.
Therefore, I would not increase your W-2 by $20,000–$30,000 and voluntarily incur additional payroll taxes solely on the assumption that it will increase your mortgage qualification by that amount. A sudden year-end bonus may not accomplish what you expect because underwriting focuses heavily on documented, stable, sustainable income rather than simply the most recent paycheck.
Your best move is to speak with the mortgage lender before changing your compensation. Give the loan officer your last two years of personal and S-Corp returns, W-2s/K-1s, and current financials if requested, and ask them to calculate your qualifying self-employment income. Then you will know whether increasing W-2 compensation would actually improve the amount for which you qualify.
So your instinct is correct: being paid a W-2 by your own wholly owned S-Corp does not ordinarily allow you to disguise the self-employment relationship for mortgage underwriting purposes.