There is the USS Gorkon (NCC-40512), named for the peace-making Klingon chancellor from Star Trek VI. It appeared in The Next Generation episode "Descent: Part I."
Also, the USS Sarek (NCC-72075) appears in Deep Space 9, "Favor the Bold."
The USS Shran (NCC-1413) honors Thy'lek Shran, the Andorian officer who eventually became an ally of Captain Archer on Enterprise.
The USS Sitak (NCC-1924) was named presumaby for a Vulcan admiral. The admiral herself appeared in the Deep Space 9 episode "Operation Return." The ship was in the later episode "Sacrifice of Angels."
The USS Khitomer (NCC-66613), from the video game "Star Trek: Bridge Commander," appears to be named after the planet Khitomer on the Federation-Klingon border. It was the site of the peace conference at the end of Star Trek VI.
The USS Surak (NCC-65601) is named for the foundational Vulcan philosopher.
Finally, there are number of ships without identifiable terrestrial eponyms. Presumably they are named after alien individuals, places, or other entities: ShirKahr (apparently a city on Vulcan), T'Kumbra, Wambundu, G'Mat, and Yolja. The last, being a Deep Space 9 runabout (which are all otherwise named after rivers) is presumably named after a non-Earth waterway.
Wikipedia has a good list of ships that have appeared in Star Trek media, from which most of this answer is derived.