I agree with the previous posts, regardless of the flavor, just make blue icing, or have some kind of blue/baby boy themed topper and you should be good. I personally am not huge on icing, so for one of my baby showers I did mini lemon cupcakes with blueberries and whipped cream topping, and I stuck a blueberry on top of them. They were cute and yummy, though not necessarily blue colored. Since the mom-to-be wants blue, maybe go with blue icing and blue sugar crystals?
There's also a fantastic cupcake blog:
http://cupcakestakethecake.blogspot.com/ maybe you can find ideas there, good luck!!