First, Balto. This probably comes from the Baltic Sea, or something to do with Baltic. There is also a theory which says that he was named after Samuel Balto, a Norwegian man.
(source : http://www.balto-iditarod.com/)

Boris is a common Russian name for a Russian goose. He also could have been named after a famous Russian writer.

Muk & Luk is the name of some sort of boots.
(http://www.stylemaven.com/styleguide_feature_mukluks.htm)

Kodi comes from the 'Kodiak Islands'.
(http://www.kodiak.org/geography.html)

Aleu is also named from an island, the 'Aleutian Islands'.

On the serum run, there was once a musher whose lead dog was named Star.

Aniu would be the Inuit word for Snow.

Sumac, is also a poison...

Finally, Kaltag is named from a town of Alaska.
(http://www.explorenorth.com/library/communities/alaska/bl-Kaltag.htm)

Updated on 17 june 2005 : I found more information on a very old Balto site! ("Balto Fan art") As it is not online anymore, I think he will not mind if I take some of it. Here's what the owner said :

I've been reading a lot of Northern history lately, specifically concerning Alaska and the Yukon, and discovered a number of interesting facts for the trivia minded as respects the naming of the supporting cast from "Balto".

The nasty malamute, "Steele", is actually rather ironically named after North-West Mounted Police Superintendent Samuel B. Steele; one of the famous contingent of Mounted Police charged with keeping order during the chaos of the 1896-1899 Klondike Gold Rush.

"Steele"'s three-dog fan club, "Nikki", "Kaltag", and "Star", derive their names from different sources. "Kaltag" is a town in Alaska that sits on the route of the Iditarod Dog Sled Race. "Star" could be a generic reference to the North Star, but could also be lifted from a tome on the Siberian Husky, in which is stated, "one should avoid giving names to dogs that are too phonetically similar to commands....(as)...the name 'Star' is too similar to "Stay", etc.", in keeping with that particular Husky's personality as depicted in the film.

"Nikki" is another venture into irony. In 1960, a subsidiary of the Walt Disney Company shot a film about sled-dogs on location in Banff, Alberta, entitled "Nikki, Wild Dog of the North". After filming of the movie wound up, the company found themselves with 200 or so sled dogs surplus to their requirements and all in need of a good home. The various dogs that played the title character "Nikki" (including "Nikki" himself), were given to the Royal Canadian Mounted Police to form the foundation of their revitalized breeding program for use in northern patrols.

And from another contributor:

Hi! I like your site and stop by often. I was reading the book Dogsong, about a modern Eskimo boy trying to keep the old Eskimo tradition alive by driving a dogsled team into the wilderness. One of his articles of clothing were muck-luck. I think they were a kind mitten or something like that. He always wore them. I think Muc is the little polar bear and Luk is the big one, but I'm not sure. Hope this helps some. :-)