"An Agony. As Now." reflects the poet's feelings of captivity and helplessness while "Black Art" is furious and pointedly divisive. The first was written in 1964, the second in 1966. As you can tell by reading the second poem, Baraka was in favor of black power, and he believed that black art should pave the way for black resistance to those in power ("Whities" and Jews). From his brusque verbiage, it's clear that he sees black art as the war cry of the black movement. He's angry even with the leaders of the black movement, calling them "negroleader" and saying that they are willing pawns of the white man: 

Another negroleader
On the steps of the white house one
Kneeling between the sheriff's thighs
Negotiating coolly for his people.

The depiction of a "negroleader" performing a demeaning sex act on a (white) sheriff clearly demonstrates what he thinks of "negotiation." He doesn't want negotiation; he wants war. 

"Black Art" is a volatile change from "An Agony. As Now.", where he is withdrawn and angry and helpless, a prisoner inside of himself. He speaks eloquently of pain and isolation, but he still believes in beauty. In this poem, his flesh is metal with mere slits to peer through; his view and experience of life is limited. The metal is hot and cannot be penetrated, thus removing him from the world, so when "hard flesh / rubbed against me, a woman, a man," it was "without shadow, or voice, or meaning." He is reduced to being a mere skeleton, which, like the metal, "is hot, it is not, / given to love." Instead, "It burns the thing / inside it [the skeleton which is him]. And that thing / screams." 

These poems are different viewpoints of the experiences of a black man caught in the chaos and violence of the Civil Rights Movement. The first reflects his political and commercial impotence, the second, his belief that rage and violence is the only answer.