Officially I dont think the rule applies to heliports since they are not often active. However its never a good idea to fly close to one, and if you do see, or hear a manned helicopter flying in your vicinity its best to bring your drone down to land in a safe place as soon as possible. Since there are also regulations for helicopters who cant fly below 1000ft in built up areas (i believe) there should not be too much hassle if you are flying a few miles away from a heliport.
However I myself am based in the UK so I am not 100% up to date with the latest FAA rules so I am honestly not sure, best if you try contact FAA directly (or read there publication on drone flying rules) to see what they have to say. On a side not you should check out this post on how dangerous a drone strike really is compared to birds