Think about the advantages:
- It can be engineered to affect only humans, leaving all other organisms unharmed.
- It is extremely efficient, feeding and replicating itself without any input from you.
- It can be engineered to be airborne, thus speeding contamination and replication, and making containment extremely difficult.
- It can be engineered to be resistant to cold and modern medicine. If some sort of quarantine is set up fast enough, just drop it in a few places. It cannot be beaten.
- If you have the ability to engineer the perfect disease, you likely have the ability to engineer another disease which can quickly eradicate it from the planet, just as easily (if necessary for some reason, once all the humans are dead, of course).
Instead of trying to outgun Earth and leaving giant craters everywhere, or trying to cripple our electronics, just sit somewhere in space the humans can't reach you, and engineer a breed of these microbes, keep a few in containment for backup purposes, and release the rest in high-population areas across the globe. For maximum spread, give it a very high incubation period, allowing it to be spread fully before any symptoms manifest themselves. To be especially tricky, make it mimic another disease or condition, thus delaying its proper identification even more.
There will still be pockets of isolated humans, especially those living on small islands. To fix this, engineer the disease to be carried by other animals, without affecting them. There are examples of this in nature (reference needed). Birds are a good candidate, as are fish for the above-mentioned islanders. Dogs could work well for isolated survivalists.
There will still be some final hold-outs, filtering their water and raising their own food where your disease can't get at it. You have two ways to get to these final survivors: either destroy them with superior weaponry, or engineer your disease to be carried via various ground mites, and thus under any walls the survivors can put up.
Inevitably, you will miss some humans. They might hide out in sealed rocky caverns or old cold war bunkers. They might even keep the species alive. It doesn't matter. They'll eventually run out of space/food/oxygen, and need to surface. And when they do, your disease will be covering the planet like an invisible blanket, just waiting for the last humans to raise their heads and take a whiff of air.
In the end, disease is the ultimate killer. If we can't stop it and we can't contain it, then there's nothing we can do.
Others have raised valid points involving the humans' deadly weapons. I don't think this is a concern though, if they never have the opportunity to use them. If you're attacking via disease, you don't need to be orbiting Earth. You don't need to be close by at all. Just launch the microbes from afar, while hiding behind a planet/moon. The humans won't even know that aliens are involved.
Even if they do somehow spot you (and even then, they have to be looking for you first if you're hiding), they can't get to you fast enough. Assuming that we're talking about modern day humans, any missiles or ships they launch will take days, months, possibly even years to reach you. You have plenty of time to detect any threats and blast them from the sky... er, space.
Another excellent point was mentioned by Henry Taylor, about the machines requiring human presence, and the animals stuck in zoos requiring feeding. This is the one problem with the disease scenario.
It's going to be impossible to save every domesticated dog, cat, and bird, so some animals will die. This should be acceptable. It's very far from eliminating a species. If you're really bent on saving as many animals as possible, the zoos are your best bet. Send down landing craft at the biggest ones once the humans are too weak/dead to do anything about it, and take over. There might be some resistance, but this can be dealt with by developing a fast-acting strain of the virus, which kills within hours. All humans within a ten mile radius of the zoo are bombarded with this strain from space, and subsequently die before they can do anything.
One problem with wiping out all humans is that certain dog breeds - specifically those with short legs, are going to be in trouble. These dogs were bred for aesthetic purposes, and won't do well in the wild when in competition with their more able cousins. Unless you start adopting these dogs, they will all die off eventually.
Another problem of killing all humans is the machinery which requires us to keep running. Even if the worst happens and these buildings turn into a gigantic ball of flame, the affected area is quite small, and the damage to the planet definitely won't be permanent. In all likelihood, all animals have long since fled from such industrial areas, so the effect on the fauna will be minimal. And if there is machinery you feel you simply cannot let blow up... just send down a landing craft and stop it.
What about nuclear power plants? According to this question on this very site, those are unlikely to go off, and even if they do, they will not turn into atomic bombs. Worst case scenario is something like Fukishima, where radioactive material is leaked into major ocean currents. And again, if something like that is about to happen, send down a landing craft to stop it before it does.
These three things: the ability to hide, the ability to send down landing craft and take over for humans where needed, and the ability to create and manipulate viruses, are all that you need to effectively wipe out all humanity. You will not find a more cost-efficient or nondestructive method.