If I live in CA and did a job physically in CA but the payment and 1099 came from a company in NY do I need to pay NY taxes?

Were the taxes withheld for CA or for NY?  If you worked in CA and lived in CA and the income taxes were withheld for CA you will only file a CA resident return.  If the taxes were withheld for NY you will need to file a resident CA return and a nonresident NY return.  

You don’t typically pay taxes with a 1099.

I did not need to pay taxes in New York because I did the job physically in California.