In a Mercury News article today, Jed York was mentioned having said that the "San Francisco" would remain in the 49ers' name should the team move to Santa Clara.

Jed York, the lead voice on the 49ers' stadium plans, made one thing clear to San Jose's Rotary Club during a speech Wednesday: Don't get your hopes up about the team becoming the San Jose or Santa Clara 49ers.
"The name of the 49ers has never been in dispute," York said. "We are the San Francisco 49ers and will continue to be the San Francisco 49ers."