IKEA has some great ideas for kids beds, don't they?
They have a "KURA" bed that starts off as a low bed with a
star-covered tent canopy, and once they are older, it can be turned upside down so that it's a loft bed with a space below for a second mattress or a play space. My older son just turned 5, and I think he might be old enough for a loft bed (or bunk bed) now, but I've held off buying it because I'm afraid the younger brother will want to get in it and fall out.
But since it's convertible, you can start it off as a regular bed and flip it to a loft later. I think 3 is way too young for a bunk or loft bed.
I would suggest a twin bed now, but that's based on nothing but my personal opinion. His tastes will probably change enough that he might want something different when he's a teen. Although he still may want a twin bed - keep in mind that college dorms usually have twin beds.
I really like the twin and full-size loft beds that IKEA has for teenagers, too, with the bed on top and study space or play space at the bottom. Very cool.