I think he isn't …: không goes in the part after nghĩ là

English often says "I don't think he'll come", putting "not" with "think". Vietnamese usually puts không where the "not" really belongs, after nghĩ là: Tôi nghĩ là anh ấy sẽ không tới. I don't think he'll come (literally, I think he won't come).

The same goes for thấy (find, feel), a very common way to give an opinion in Saigon: Em thấy cái áo này không hợp với chị. I don't think this top suits you. For a guess, use chắc (probably) with không: Chắc mai trời không mưa đâu. I don't think it'll rain tomorrow.

Tôi không nghĩ là … also exists, but it sounds stronger, closer to disagreeing: "I really don't think …". Tôi không nghĩ vậy is the natural reply when you disagree with something just said: I don't think so.

Là after nghĩ is often left out in speech: Tôi nghĩ anh ấy sẽ không tới. In writing you'll see rằng instead.