The ones (those) who are no longer with us. (this is what I say) The ones (those) who have gone.

As previously stated, "the ones who are gone" is the appropriate one of your two options. I should say, though, that "gone" is a bit more general, so you'd need add some more context in order to distinguish the meaning from the person simply having left a place.

Thank you guys for answering my question! I really appreciate it!

The first sentence "The ones who are gone" would refer to a number of people who have died or passed away. The second sentence "The ones are gone" would refer to a number of things (not necessarily people) that are gone. When "Who" is included in the sentence we know that we are talking about a person or people.

It would be "the ones who are gone".