The boss' wife is our "bookkeeper" (if you can call her that). Anyway, the amount on line 1 of my W-2 is different than lines 3 and 5 (Social Security wages and Medicare wages respectively). Can this be correct?

Yes, You may have had pretax deductions.

Yes, they can be different.

In some states, like NJ, the Box #1 figure will be different than the Box #16 figure.

This is not unusual - I don't think my box 1, 3, and 5 have ever agreed since my last summer job as a college student. There are many reasons these amounts may be different. In my case I find that my box 1 Federal wages is basically my wages minus withholdings for pre-tax deductions for things like my 401(k) contributions, medical and dental insurance costs that I pay, and my medical savings account. Box 3 is like Box 1, except it adds my 401(k) contributions back in, and also adds the value of the group term life insurance that my company provides for free but is above what the IRS thinks $50K of term ought to cost. Box 3 is like Box 5, except it is limited to $97.5K max. If you have other things going on, such as if you received a reimbursement from your employer for relocation or a per-diem, this can lead to additional differences.