Translation:The ice cream, which has chocolate in it, is melting.
Joka is nominative.
Your sentence could, for example, be "Jäätelö, joka on suklaanmakuinen, sulaa.". Words with -makuinen are among those pretty rare compound words that you can write either together (suklaanmakuinen) or apart (suklaan makuinen).
But most likely, we'd just say "Suklaajätelö sulaa". :-) (This compound word you can't write apart.)
EN-AUS speaker. Leaving that preposition dangling is wrong in my dialect too. It has to be "in it".
After trawling the web for a bit, I think it's safe to say it has to be "in it" in most forms of British English too. It doesn't make any sense to say the grammar of someone's idiolect is wrong but this suggestion is clearly non-standard.