We're using Playtex drop-in bottles, and they say not to microwave. I don't know much about bottle warmers because our daughter would drink room-temperature milk until just recently (she's 1 y.o. now and we're trying to get her to sippy cups rather than bottles).
The only two ways I've tried are (with 1 being my preference):
Heating up water in a coffee mug, then putting the milk filled bottle in the coffee mug full of hot water. (This keeps me from heating up the milk too hot)
Heating up the milk in a microwave safe container, then pouring that into the bottle liner. I've gotten it too hot this way a few times and had to cool it off.
Never heat the milk in the microwave, even in a separate container. This can create hot spots that can scald the baby. We always use your first method but we just use hot tap water. Remember, it just needs to be slightly warmer then body temp.
We bought a miniature crock pot that we leave plugged in and full if water. It's hot enough to heat a bottle quickly when immersed, but won't overheat the milk unless it's left in there a really long time. Once I take it out I give the bottle a quick shake or a few swirls to evenly distribute the temperature.
It can take a while for hot water to come from our tap so this method is much faster and saves water.
My personal preference is for the microwave -- use a similar container and a formula for the amount of time you run it (I generally do 6-7 sec./oz). If it comes out too hot and you need it right away, poor a (very) little bit out and replace it with cold milk.
Note: it only takes a small amount of cold milk to offset overly warm milk, so there is a risk of overdoing it a little.