Can I make a large SEP-IRA contribution using W-2 income? I'm an independent contractor and it's from a NQSO. I paid FICA taxes. Boxes 11,12 are empty on my W-2.

You can only make a SEP-IRA contribution through your employer. If your income is reported on a W-2 form, only the company that issued the W-2 could contribute money to a SEP-IRA set up on your behalf. You may be able to make a deductible contribution to your own IRA, however.

Thanks for the thoughtful answer. It's only some of my income. I have other income. 

How about a Solo 401k then? I guess what I'm not getting past is that I am not employed by the company. Have't been for years. Why can't I contribute as my own employer? 

The Small Business and Self-Employed Tax Center includes Retirement Plans. If you have positive business income you can contribute. Choose a plan that suits your business and go for it! Both links have great information.