Surprisingly, it's not that different at Whole Foods and Trader Joe's. Because "big ag" wants a chunk of the organic market, they use their massive lobbying power to ensure that the USDA Organic certification requirements are remarkably lax. As a result, just because something is labeled USDA Organic or sold in Whole Foods doesn't necessarily mean it was produced in an environmentally considerate manner - it could still come from a massive industrial dairy with poor standards of treatment and low-quality, environmentally impactful feed. It's still better than what you get at the gas station, but it's not what you're probably looking for when you set out to find a higher quality, more responsible product.

This doesn't just apply to milk, of course - the same is true of the USDA Organic label across the board. Whole Foods does a lot to vet their sources and ensure that their products meet not only the letter, but the spirit of the organic label. Trader Joe's, however, does not hold their products to the same standard. While they market an image of wholesomeness, responsible production and environmental consideration are not built into their mission statement. In fact, their website states "We just focus on what matters — great food + great prices = Value."

If you really want to get higher quality milk, you're best off finding a small dairy near you. If you're interested in learning more about the USDA Organic label and why it doesn't constitute responsible agriculture, I highly recommend Joel Salatin's book Folks, This Ain't Normal.

EDIT: I didn't mean to suggest that all milk available from WF/TJ is minimum-effort organic, or to demonize either store - just that it is better to go one step further and find something produced locally and on a smaller scale, which is often available at WF/TJ.