Just kind of thinking out loud here, but there seems to be to be a major difference in the historical time frames for the two types of literature. Fantasy, to me, seems to have a direct antecedent in the fairy tales that were told throughout the world for the last several thousand years or more; also in things such as the mythology of Greece, and the legends of Arthur et al in England. Science fiction is a much newer type of literature (going back to what, Shelley perhaps? And becoming more widespread through Verne and Wells.).
Tolkien seems to have, in the public's mind, the reputation of being the author who mastered fantasy...he brought it to what many see as its highest level of accomplishment; it was masterfully written by a renowned Shakespearean scholar. TLOTR is an all-time classic and the way to consider it is to consider its influence on the writing of all fantasy that came after it.
Science fiction was perceived as junk literature throughout the first half of the twentieth century (with the exception, perhaps, of only Wells); it was pulp, it was looked down on by almost everyone...authors of most other genres, teachers, parents. It was with works such as Asimov's Foundation series...Heinlein and Clarke's novels...and books such as Dune in the 1960s, that science fiction began to be accepted by a wider audience as a legitimate form of literature. So another way to consider the most successful works of science fiction is to consider what authors and books had the most influence in making science fiction popular, and acceptable to those who before had ridiculed its worth. I guess I'm wondering if, with science fiction, it's not more proper to consider what books influenced other authors to imitate their styles in the attempt to write works that would sell, rather than works that would uplift the genre. From what I've read of the realities of SF in the 1930s through mid 1950s, it was more about quickly churning out masses of words to the pulp magazines to make a few bucks, than it was about writing enduring classics that would change the direction, and reputation, of the field. Maybe I'm saying that the genre isn't old enough yet to have that one certifiably unique masterpiece-of-influence.
I may not have made any sense at all.