I like
Zoe best. I like it even better with the diaeresis on the E but I can't do that on my keyboard for some reason. It would probably make things more complicated but I like the way it looks.
Zoey isn't horrible but it is not nearly as beautiful as
Zoe. Zooey looks terrible, is very Deschanel and should be pronounce ZOO-ee (like Zoo+ee) for logical reasons. Ugh. I know it has been used in literature but that doesn't really make it better. As for alternate spellings I think
Zoie and
Zoey are ok but not great. I'd stick with
Zoe.