As a NY fulltime, year round resident, I started freelance/contract work for a California based company and will receive a 1099-MISC form for the fees they pay me. Will I have to file a CA non-resident income tax return in addition to my NY resident return? I assume yes but a few people have thought no because I am a) not an employee who will receive a W2 and b) never physically work outside of NY.

I reviewed this topic before writing this so many thanks for the explicit advice. Also, apologies if this shows up twice, I thought I entered it a little while ago but it doesn't seem to be showing up.

If you were never present in CA to do the contract job, then you do not pay any CA taxes or file CA tax return. You will report this income on NY tax return.
How you will treat the 1099-Misc income, read: Your U.S. Tax Return: W2 vs 1099-Misc: Employee vs Independent Contractor. (http://taxipay.blogspot.com/2008/03/w2-or-1099-employee-or-independent.html)

Agrred; in this case, it is your physical location while working dictates to whom you owe state income taxes.