Since you are paying yourself a salary, I'm assuming your are organized (or at least taxed as) a S-Corp.
SEP contributions (and the employer contributions for SIMPLE IRAs and 401ks) are based off of earned income, which in your case are the wages you pay yourself. Unless you are paying yourself a particularly high salary, a 401k will allow you to contribute more for retirement as you can defer $18,000 from your wages, plus have the employer contribution of up to 20% of wages or the cap of $53,000, whichever is less.