For the most part they're the same thing. However, a letter of recommendation is usually much more personal and people refer to it more often in an academic setting. A letter of reference is a bit less personal...usually when you apply for an average job, they want a letter of reference from your former employer to see if you're trustworthy. Sometimes, I see letters of reference in forms of circling and checking the boxes, and they evaluate you from there.
I know of an entire website that deals with the differences and similarities between recommendation letters (letters of recommendation) and reference letters (letters of reference).
It also gives a lot of info and tips on how to write the various types.