The couple, who are parents to three children, looked relaxed during the dinner, reported Us magazine.
"They were drinking red wine. They looked relaxed," a source said.
"No one was really bothering them at all -- they were really normal, they fit in," the source added.
Affleck is in the city to shoot 'Batman vs Superman: Dawn of Justice'.
The pair tied the knot back in 2005 after falling in love on the set of Daredevil. Garner was previously married to her Alias costar Scott Foley while Affleck was previously engaged to Jennifer Lopez.