Have a Finance Question? Ask a Financial Expert Online.
It would be better to sell the stocks as the amount of tax you will need to pay will be less than if you take withdrawals from your SEP IRA. The taxes due on the sale of stocks will depend on the amount of gain that you have on the stocks and the period of time you have held them. Only the gain will be subject to taxes. If you held the stocks for more than 1 year then the gain will be taxed at long term capital gains tax which is either 0 or 15% (or a blended rate).
If you withdraw from the SEP then the entire amount will be subject to ordinary income taxes (assuming you have not made any after-tax IRA contributions to any IRA accounts).