As a long time and continuing NJ resident I worked 95 days in NY in 2011 prior to being laid off. I've also received approximately 6 months pay as a severance payment. Do I need to use schedule A to allocate approximately 9 months of wages against 95 days of employment in NYS?

You file New York's IT-203 as a non-resident, to document and pay taxes on your NY sources of income (your wages plus NY unemployment). For NJ you file NJ1040 as usual, reporting all income for the year and claiming taxes paid to other jurisdictions using Schedule A.