You can think it's a girl's name all you want, but when a name literally means "son of Emery," there is no opinion on the subject.
If you want to use it, then own it. Spell it correctly. Emerson. The other choices make me cringe.
Yeah the reason "some people think it's a boy's name" is because it IS a boy's name. I can call a cow a sheep, but it doesn't change the fact that it's a cow, everyone will know it's a cow, and people are going to look at me like an idiot.