He reports to Rosenstein and Sessions, but Sessions has recused himself. He’s paid by the DOJ. The DOJ is part of the Executive Branch and answer only to Trump. This is definitely within Trump’s area, he just has been threated by congress-critters to leave Mueller alone or they will try to impeach.
Sessions should replace Rosenstains #2 and #3 with affirmative action picks
Then Trump should promote Rosenstain out of his present job
Note to future presidents: Get every Cabinet and agency head and their deputies to write letters of resignation before the inauguration
Then choose which ones to accept by sundown of inauguration day