Mr. Lif is a Boston-based rapper who writes primarily political songs. His songs are consistently engaging and hardcore; he’s obviously a fan of Chuck D.
Mr. Lif - Home of the Brave
Mr. Lif - Because The Made It That Way
Justin Warfield is a multi-talented singer/songwriter/musician. I think he’s touched on every style of contemporary music there is, with the possible exception of bluegrass.
Justin Warfield (here performing with Bomb the Bass) - Bug Powder Dust
Kool Keith is one of the most prolific, intelligent, literate and downright crazyass rappers ever. He’s always fun and interesting to listen to, and his subject matter often makes him seem like a rapper version of Sun Ra.
Kool Keith - Rockets On The Battlefield (one of my all-time favorite tracks from this guy)
Kool Keith (recording with Material, a Bill Laswell project that featured lots of different rappers and DJs) - Conspiracies
Last, I don’t know if this is the type of “intelligent” rap music the OP is looking for, but for my money, there has never been a rapper as creative and as playful as Chip Fu of Fu-Schnickens. To be sure, his two mates are competent as hell, but Chip is a step above all other rappers. No cursing, no bling, no bitches, no hos, no busting caps… nothing but phat fast raps. But it’s not just his lyrics that are playful, it’s his delivery itself and the general attitude of the band. Rap like this just doesn’t exist anymore.
Fu-Schnickens - What’s Up Doc? (Can We Rock) (K Cut’s Fat Track Remix)
Fu-Schnickens - La Schmoove
Fu-Schnickens - True Fuschnick
Should I list more? I have quite a healthy collection of rap music, mostly from the '80s and early 1990s, and it’s quite different from what passes for rap nowadays.
Okay, two more, just because I love both of these tracks; they’re incendiary and intelligent and straight up outstanding:
2 Black 2 Strong and the MMG - Burn Baby Burn
Movement Ex - Freedom Got A Shotgun