Michael Pollan’s book, the Omnivore’s Dilemma, deals explicitly with this dual problem. There is no clear cut answer and potential harms vary widely on a case by case basis. On a practical level you may just have to use your best judgement based on the choices available. Often you can get both local and organic in one product. On the other hand, if you have a lot of time to kill and can do the research to fill out their forms you can look at this food carbon footprint calculator:
There are advantages and disadvantages to buying locally. It is true that locally grown food may not be organic, while the organic foods are shipped from far away. Also, the different types of food have different levels of impact on the environment. For example, local, organically grown and packaged beef can still be worse of the environment than vegetables that were grown far away and packaged in non-recyclable materials. You really have to calculate the cost for every individual item.
Unfortunately, it is very difficult to calculate an eco-footprint that measures all of the different facets of food production and transportation. The first link below has a table that calculates and lists ecological footprints for various foods in terms of global hectares. The second link below is to an article that details a natural experiment about sustainable food growth. If you have the time to read it, I highly recommend it.
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