Low flying subsonic cruise missiles can easily be engaged with air to air missiles, but enemy aircraft would be a higher priority... especially before they launch their weapons.
Cruise missiles would be fairly easy to detect with IRSTs tracking their heat trail, and of course AESA radars can look down fairly easily... any model MiG-29/35 or Su-30/35/34 can easily outrun a low flying cruise missile... even if they had to climb to medium altitude to accelerate and catch up...
Who engages what would largely be decided by the IADS... that is what it is for, but a flight of MiG-35s could certainly fire off AAMs at any enemy air threats and then turn and chase down some low flying cruise missiles and engage them with cannon depending on the situation.
Of course Russian ships on the Black Sea could also offer missile and gun support, but when it comes to engaging stealth aircraft the Su-35 and Su-57 have the advantage of wing mounted L band AESA radars to detect stealthy objects, which the MiGs lack AFAIK.