Sometimes Old Navy, sometimes Children's Place, Carters, Oshkosh have tiny sizes for their shirts. There are a lot more options starting around 12 months+ if you're looking for something beyond the newborn kimono-style shirts. I hate onesies so looked quite a bit for DS.
There is this French brand called petit bateau that makes onesies that look like big kid shirts - it's really cute actually. So you get the ease and comfort of a onesie, but the bottom part of onesies is "hidden" by pants while the shirt top part of onesie goes over the pants. A couple of other European brands also make big boy clothes, some of the Gucci for baby clothes aren't bad, I like Petit Bateau for the cute factor.
Re: Baby boy shirts(no onesies)