This is tough, since both
Jonah and
Benjamin are among my absolute favorite boys names.
I will cast my vote for
Benjamin here because I don't like the combination
Jonah Eli. I don't know, I've never cared for
Eli,
Elijah,
Isaiah,
Elisha etc.
Between
Benjamin Andrew and
Benjamin Henry I pick
Henry because it's the more unusual combination.
What about
Benjamin Jonah or
Jonah Benjamin, though?
And since it seems to be en vogue these days, why not go with 2 middle names?
Jonah Benjamin Henry or
Jonah Benjamin Andrew are nice, too :)