Is the coffee here? makes sense if you already know that there is coffee somewhere. Is there coffee here is asking whether or not you have it at all. Eg. Someone is providing coffee to your office meeting. When you arrive you ask "is the coffee here?" Or You are looking in the cupboard and ask "is the coffee here"? And are told no, its in the cellar.
Not one, but two of my native Russian friends say this is odd and they would never say it this way. One lives in Moscow and the other in St. Petersburg. To say specifically "Is the coffee here" they said it would have to be something like "Это тот самый кофе?" or "Здесь есть какое-либо кофе?" I got the impression that they were implying that "Кофе здесь?" is kind of, sort of like broken English. But taken out of context, there is nothing in this phrase implying some specific coffee, therefore it seems that translations like "Is there coffee here should be ok.
I'm not a native, but I immediately translated that as "Здесь есть кофе?".
In Russian, different word orders give different emphasis. In "Здесь есть кофе?", you are asking if the coffee exists (hence why the "есть"); while in "Кофе здесь?", you know that the coffee exists, so you're asking if it is in a specific location