The rules for Seafarers (pdf) do not address combining the two expansions. The rules for Cities and Knights (pdf) do address combining the two games (page 13), warning that only certain scenarios work well, and providing rules for things like how to treat ships as roads and how a knight can chase away the pirate. They do not, however, specify how many victory points to play to. The FAQ on combining the two expansions addresses a few questions, but not the victory point question.
There is a thread on BoardGameGeek about combining the two expansions, in which two separate people mention that the official rule is to add 2 victory points to the Seafarers scenario if you're playing with Cities and Knights. According to Daniel Johnson:
Also, Klaus Teuber's website has a FAQ at http://www.klausteuber.com/en/index.php?page=seefahrer_staedte_und_ritter.html with a few questions that might not be answered by the Almanac.
2. The victory point goal should be 2 more than in the Seafarers scenario.
Sadly, the site linked to seems to have been reorganized, and that link just redirects to the home page of catan.com. However, this seems to be the best answer that is available so far; to add two victory points to the conditions listed in the Seafarers scenario.
I have never tried this, as I tend to prefer not to combine expansions in games. I find that in general, combining too many expansions makes a game bog down too much. I love Seafarers, and find Cities and Knights nice too, but combining them would just add too many extra things to think about, and too many confusing interactions (like this one) that need to be answered in separate rules, FAQs, and the like.