As Martha said, they are so different from each other. And I like them both too!
Bob Dylan is a poet in the original sense of the word. He plays with language, using metaphores, abstract it, etc. At times he even writes impressionistic (Tangled Up In Blue is a good example of that). While this creates some wonderful songs, at times you really wonder what he's trying to say in certain songs. This should of course not prevent someone from enjoying it, but it may cause someone not open him/herself fully to the song.
Lou Reed on the other hand is a street poet. His language is from the street. There's no flowery beating around the bush, it is clear what the words mean. Here you can really see the influence of Delmore Schwartz (try to find his story In Dreams Begin Responsibilities and see how he can tell a great and moving story in 7 pages). As a result, Lou's songs are easier to get into (lyrically speaking). His gift is that he leaves out all the unnecessary stuff, so you keep captivated by his stories.
Now, as to which one I prefer, I can't say. I may listen a bit more to some Dylan records, but to me Lou Reed has written the greatest song ever (Magic And Loss from his Magic & Loss album). Both are superb lyricists, although coming from completely different directions.
No, choosing one would be unfair to the other. I take both!
Marty