The externalities of alcohol consumption can be largely mitigated by drinking in moderation.

The primary externality of smoking, secondhand smoke, can be mitigate by having people smoke outdoors, which most countries already require in public spaces.

The main secondary externality of smoking, increased strain on the healthcare system, is more complex. Smoking is more addictive than alcohol, so moderate consumption is less possible. Therefore, smokers are more likely to experience an illness directly related to their consumption than alcohol consumers.

In America, I'd suggest this externality could be addressed by removing the cap on the smoking health insurance surcharge (it's currently 50%). In countries with socialised medicine, this could be better addressed by adjusting cigarette taxes to fully reflect the average lifetime cost of treating smoking related illnesses.