Hi there,
I live in Northern NY State and I telecommute to a company in Atlanta, GA. I work out of a home office... where do I pay state taxes? Right now my employer has been deducting and paying taxes to GA. Is this right?

Since you work in New York (from home) your nexus is NY. As such file in New York and advise employer of same.

Agreed. File a GA tax return as a non-resident with NO GA income to get all the taxes back, then file a NY state return and pay NY state.

Expect to pay an under-withholding tax penalty. NY state may waive it if you ask, but I would not hold my breath!