This may not be a problem – and if it is, it's most likely not yours anyway. It's entirelly possible that there is some context, that makes this acceptable. For example, perhaps he just got promoted or became a father, and his manager spiced up his coffee as a sign of cammaraderie and to congratulate.
As a fellow developer, and former worker in the restaurant business, there have been many acceptable situations where I have been consuming alcohol (in moderation!) while at work (celebrations, friday night team meetings etc.). In some cultures, this is entirelly okay, and some times it's even expected.
Also, don't forget that some medicine, such as cough syrup, contain alcohol. Adding a splash of whiskey to a cup of honeyed tea is a common remedy for a cold or sore throat, when cough medicine is not available. Although perhaps you can argue for his poor judgment, it doesn't make him a drunk.
You say that you definitely smelled whiskey in his cup ... but how sure are you? Is there a tiny chance that you might in fact be wrong? And even if you're not, and we assume he has no good excuse to spice up his cup o' joe, do you have any proof? If not, it's your word against his, and you'll look like a fool.
Nobody likes a tattle tale, and this sounds like a minor problem anyway. Drinking on the job is probably not great, but unless he is heavilly influenced, consistently shows up drunk or there are other issues (e.g. he is a brain surgeon or customer service rep), I would keep this to myself.