The available sources on Norse mythology do not seem to give much importance to (for a lack of a better term) "biological relations". Instead, they place a lot of emphasis on the "function" of characters. Hence, Loki is never referred to as a Jötunn, despite being the son of the giant Farbauti (the category of beings to which his mother Laufey belongs is never specified, although there is some consensus she was a goddess). Instead, Snorri explicitly places him among the Aesir in Gylfaginning. Keep in mind that Odin himself, being the son of the giantess Bestla, would be "biologically" half-giant, but this takes nothing away from his function as head of the Aesir.
Moreover, and perhaps most importantly, Loki is presented as a shapeshifter, even going as far as taking the appearance of a mare and giving birth to Odin's horse Sleipnir (source again is Gylfaginning in Snorri's Edda). It shouldn't then come as a surprise that a serpent and a wolf are part of his offspring too.
In conclusion, Fenrir and Jörmungandr are never called Jötnar in the available sources. They are instead referred to according to the function they fulfill, i.e. that of "monsters". Or, as the specific kind of monster they represent: a worm, or serpent for the latter; a wolf, or warg for the former.
EDIT (to include more information on Jötnar):
Also, a little comment on the humanoid appearance of Jötnar. This is not always the case, as there are several instances, for example, of giants with many heads (e.g. Tyr's grandmother, Aurgelmir's son, and the nine-headed Þrívaldi). The thing is, there is no "canonical" description of Jötnar in the known sources. Some are described as beautiful and assumed to be humanoid (like Gerðr), some as monstrous and with clearly non-humanoid features (like Tyr's grandmother), some are made of stone (like Hrungnir), and others are known to shapeshift (like Þjazi).