I have never seen any indication that Gaiman and Pratchett's work was used as the basis for Supernatural's Crowley, and the similarities between the two characters are mostly superficial.
Crowley from the novel is a demon whose existence dates back at least to the Garden of Eden; his name is just a modernized version of "Crawley" ("Crawly", in the novel), since he was the serpent from that story. He lives on Earth, is friends with an angel, and is largely content to keep living the life he has.
Crowley from the show is a demon whose existence dates back about 350 years, and who was originally human. Prior to about the 4th season, he spent most of his time in Hell, travelling up to Earth to make deals and collect souls. While he does try to prevent the apocalypse from happening (like his counterpart), he does so primarily to gain more power for himself, and ultimately seize control of Hell from Lilith. His plans later on in the series include an attempt to open the Gates of Hell and let his demon army loose on the Earth, which is arguably worse than the Apocalypse, where the general consensus is that Michael would have won in the end.
As far as the similarity in names, there is a very prominent figure in recent occult history named Aleister Crowley, who shows up rather frequently in pop culture. For those people who aren't familiar with him, the name is often associated with "Satanism" or "witchcraft", making it a good choice for a vaguely evil sounding name.
For the record, that categorization of the man is pretty far off base. The guy was a bigot, not to mention (IMO) out of his mind, but he wasn't "evil" so much as he was a "proponent of individual morality." He refused to even accept the idea that Satan existed. But few people know anything about him other than Ozzy Osbourne wrote a song about him that sounded creepy.
