HSA contributions are pre-tax for both taxable wages and for SS/MC wages so using box 1 vs box 3 (or box 5) will not tell you if the HSA is pre-tax.  Get the year-end paystub.  Do the math on gross pay to taxable wages.  You'll subtract out (typically) health insurance, dental, vision, etc., FSA and HSA to get from gross to W-2 box 5, then subtract 401(k) to get to box 1.

Rick