What's the best way to take my home office deductions if I work at home both as an employee (and get a W-2), and as a contractor (and get 1099s)?

Claiming a home office as an employee is done using Form 2106, which is reported on Schedule A under the category that is limited to 2% of your Adjusted Gross Income (AGI).  So, it may be more difficult to get a tax benefit claiming it that way.  (See the Note below)

Claiming a home office as an independent contractor reporting income and expenses on Schedule C may also have its limitations if the business does not have an overall gain or if the time spent generating income from the home office is not significant enough to allow the home office deduction.  However, if the home office deduction is allowed and not limited, claiming it with Schedule C will reduce your self-employment taxes, so it is probably the better choice overall. 

Note:  Due to the Tax Cuts and Jobs Act, claiming a home office as an employee is no longer an option.  Employee business expenses claimed on Form 2106 are not deductible starting with the 2018 return through 2025.  Claiming home office expenses on Schedule C was not affected by the Tax Cuts and Jobs Act.

[edited 3/13/2020 | 9:31 am PST]