MS/EQ will be effective against Regirock and Registeel, as well as against Dialga and Heatran in Gen 4. Of those, MS/SB will only be effective against Regirock, but due to SB's extreme base damage it outpaces EQ despite lack of STAB. It's also stellar against Thunder variants of Kyogre and non-SB variants of itself, should they return to raids.
Personally I have one of each powered up to level 30ish, but if you're looking for something effective against more incoming bosses then EQ might better benefit you. Both of them do have their places though.
