The first option is correct.
Most of these products do not list the source of that ingredient, so one
must ask the producer from where that ingredient comes.
Alternatively, if you want to put "from" at at the end, that is also perfectly acceptable.
Most of these products do not list the source of that ingredient, so one
must ask the producer where that ingredient comes from.
All you need to beware of is that you don't have "from" twice in the sentence; it moves, it doesn't double-up.
The aversion to ending a sentence with a preposition is not a rule, it's more of a guideline - meaning you can ignore it if it means your sentence doesn't flow.
Probably the most famous example of this is a 'joke' quote, usually [mis]attributed to Winston Churchill.
It comes in many forms & like 'Chinese Whispers' changes at every telling.
The basic form is
That is a rule up with which I will not put.
Many variations on the theme can be seen at “Churchill” on Prepositions
The 'joke' comes from the treatment of each word which could possibly be considered a preposition & then moving it so it's no longer at the end.
Google "up with which I will not put" for a plethora of examples.
Also see, from English Language & Usage SE - “[…] up with which I will not put.”
You can choose which word you need to end your sentence with.
... or you can choose with which word you need to end your sentence ;-)