Personally I think sf/fantasy novels (or practically any novel for that matter) can be as long as the writer needs them to be -- just look at Harry Potter! On the other hand, there might be a few factors that might affect your chances of being published if you're a first-time author. Publishers need to invest money in all of their authors and if the production cost of your book becomes too high simply because of your word count, that might affect their decision to take you on or not since you haven't proven that your work can sell well yet (By contrast J.K. Rowling, being a proven commodity, is probably encouraged to write long mss to up the price, but that's just speculation on my part). I've heard conflicting arguments, but in general I believe 40,000-60,000 is the average word count for Middle Grade books while 50,000-90,000 is average for YA.
Another thing to consider is that your long book might be able to be split into smaller volumes and be marketed as a trilogy or multivolume series. I believe J.R. Tolkein originally intended Lord of the Rings to be one book but was persuaded by his writer to make it a trilogy. Again, that decision is something that depends on the editor (and you)