The 5498-SA will report on the total contributions to your HSA from all sources.

Your W-2 reports (in box 12 with a code of W) the sum of the amounts that your employer contributed and what you contributed by means of payroll deduction. It will not include any amounts you contributed directly to the HSA outside your employer (but the 5498-SA will).

Since the 5498-SA came from your HSA administrator, they are in the better position to know what amounts were actually contributed. 

Compare the detail of your HSA account (probably available online) with your W-2 - if there are discrepancies that aren't explained above, you need to start investigating.

All of my HSA contributions come through my employer - they are taken directly out of my paycheck. I have contacted my HSA to try to figure out the difference but all the contribution listed are through my employer. If I'm reading this correctly, I should determine my excess contributions on the 5498-SA and ignore the information on the W-2 as it grossly under reports what is stated on the 5498- SA?

No, do not ignore information on your W-2 - a copy is sent to the IRS who will eventually compare it to your return and write you a letter if they see an unexplained difference.

Instead, ask your employer why the amount that the HSA administrator says that they received for 2017 is different than what they reported on the W-2 in box 12 with a code of W. Sometimes, employers mistakenly add their contributions to the code W, but not the employee's contributions by payroll deduction, and vice versa.

May I assume that box 1 on the 5498-SA is blank, and that box 2 reflects all the contributions that were made? If so, ask the employer why their W-2 number is different - and if they discover a problem, ask for a corrected W-2, so that the IRS is updated and you can correctly finish your return.