My son has a bookshelf full of stuffed animals. I am not sure what you mean by stuffed animals being too girly. Most of the ones my son has look like mini versions of the real animal. My son loves learning about real animals, and just about everyone we know has given him stuffed animals.
There are several children's books that have matching stuffed animals. The series "If you give a mouse a cookie..." has several different stuffed animals that match the stories: a mouse, a cat, a moose, and a pig. The pig is a girl in the story, but my son still loves it. There is always the Philadelphia Chicken, if he likes farm animals. There is a book and CD that go along with it. My son still loves listening to the CD. The music is funny and sarcastic, not an annoying children's CD at all.
Why don't you let your son choose which stuffed animal he would like to sleep with? When our son transitioned from his crib to his bed, we told him he could get a new friend to sleep with him at night. We explained that his new friend had to be soft and not have any hard parts on it. If you are worried about certain kinds of stuffed animals then give him a few choices that you are ok with him choosing.
If you let your son choose his friend, he will breathe life into it. My son's lovey does everything with him. They sleep together, eat meals together, play together, read books together, learn ABCs together. My son's lovey is in need of some patchwork again. He has had two patches so far from being loved so much. Let your son choose, and whatever he chooses will probably be around for years to come provided you can patch it up. (Sewing is not my strong-point. But I can tell you that the love you have for your kid can help you do anything. I kept praying the entire time I patched his lovey up that God would do the sewing for me. And you know what? The threadbare parts got covered, the ripped seam got mended... I don't know how to sew, but I did it. My son just sees his best friend, the love of his mom mending it, and how faith can help you achieve something difficult. My only advice other than letting your son choose his own stuffed friend, would be to make sure the stuffed animal is well-sewn together.)
Hope your son can find the perfect stuffed friend.