San Francisco is considering a comprehensive smoking ban in public areas — except for medical marijuana. San Francisco already has limited outdoor smoking around cafes and restaurants and near building entrances and vents.
Even with a “prescription” for marijuana, federal law and most state laws prohibit possession, smoking, or otherwise consuming marijuana. New York law specifically prohibits the burning or open possession of marijuana. It is a B misdemeanor in New York. Police in New York City are actively arresting people for this. New Jersey law has approved medical marijuana, but has not approved any medical marijuana distributors nor has it approved any regulations for its consumption.
Bottom line: despite what San Francisco may be doing, marijuana is still illegal in New York and New Jersey.