3 of my favorites too. You might try 'Elephant Tree' and 'Mars Red Sky'. But really those 3 bands have no contemporaries I've found that aren't poorer imitations. For that you could look at 'Rishloo' and 'Soen' who are both Tool soundalikes.

Nobody can replace Zack de la Rocha, so you could check out his early stuff with 'Inside Out' and the 'one day as a lion' EP. Also give 'Rollins Band' a try, starting with Low Self Opinion.

Assuming you like the early Beastie Boys stuff, rather than the Intergalactic era, than maybe 'Eric B & Rakim', 'Jungle Brothers', 'Wiseguys' & 'Funky 4 +1'