For letters of rec, I think the most important thing is a very strong letter (or preferably plural, letters) from undergrad professors who can attest that you can do strong academic work -- even if it is not in this field. Ask around, but my gut would say that if you go with three letters, you should have two letters from undergrad profs who knew you well and can say what a smart, good student you are, and one should be from somebody (not necessarily a professor) in this field who can attest to your experience and passion.
That's generic advice. Sometimes it varies with field. (For example, the advice I just gave would be pretty good for law school. It would be less good for grad school in mathematics, where three professors would probably be a better idea. But my guess is it's good advice for agroecology).
One thing I'm noticing on these pages, by the way, which is unusual in the fields I hang out in, is that many of the departments are strongly encouraging or even requiring that you contact and talk to faculty members before applying. Look carefully at any programs that you're interested in and see if they require this. An example is here:
http://nres.illinois.edu/graduate/future/apply ("All applicants are strongly encouraged....") I'm seeing similar stuff elsewhere, but not everywhere. (Berkeley explicitly said it is not required).