They're both gorgeous. I prefer Naomi because I think the pronounciation is more intuitive. Noemi is more unusual and I think a lot of people would comfuse it with Naomi, which is pretty common here.
Naomi's more natural to me and standardized, but Noemi's ok. I like the sounds for Naomi better- whether said Na-o-me, Nay-o-me or Now-me. It's prettier.