Migration into multi-value field collection
I ended up writing a drush command to run before the migration that would take the 'ingredients' field from the source db and create a new table with the ingredients each parsed into their own row and a delta column to keep them in order. I then configured the ingredients migration to point to this table instead of the recipe table.

My DB connection for this migration ended up looking like the following:

$query = Database::getConnection('default', 'legacy')
  -&gt;select('_recipe_ingredients', 'i')
    -&gt;fields('i', array('id', 'recipe_id', 'ingredient'))
    -&gt;orderBy('i.recipe_id')
    -&gt;orderBy('i.delta');