Lauren and I made ice cream sundaes at home a few weeks ago, and we wondered about the origins of the word. It turns out it's one of those ones that does not have a definitive etymology. From the OED:
The name is generally explained as an alteration of Sunday , either because the dish originally included leftover ice-cream sold cheaply on Monday, or because it was at first sold only on Sunday, having, according to some accounts, been devised to circumvent Sunday legislation. The alteration of the spelling is sometimes said to be out of deference to religious people's feelings about the word Sunday. For several accounts see H. L. Mencken, The American Language Suppl. I. (1945), pp. 376–7.
Unfortunately, I couldn't find a copy online of Mencken's explanations. The theory about Sunday legislation seems to come from a place that banned ice cream sodas, prompting someone to offer the treat without the banned soda.