From what I've seen, Skull and Bones seems more naval combat oriented, while Sea of Thieves is more about exploration, but at sea and on land. Although they're both pirate themed, gameplay wise, they don't seem very similar.
Although both offer naval combat, again, Skull and Bones seems to focus more on it while dumping everything else that the likes of Sea of Thieves and Black Flag have to offer. I suppose if you're all about naval combat Skull and Bones may be your bottle of rum.
Don't really have an interest in either. But if I had to choose, I'd be more interested in Sea of Thieves. A naval combat focused game where the open world is just sailing in the water doesn't sound very fun to me. I don't think this is the dream pirate game people were asking from Ubisoft that is Black Flag but without the AC.