The $660 that was in box 12 on your W-2 with a code of W should be on form 8889 on line 9 - employer contributions.
If it is not, then you have another issue...
As for New York City, it would take me quite a while to build a test case for this to even see that worksheet (and today is not a good day for that), but this amount should not be added to City income (if that is what it is doing). Feel free to zero it out if you can, and document whey you did it for your own records.
The HSA contribution should not be an adjustment (either way) to federal income (or state income).
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