You're right: native speakers do use both forms. The standard version is this:
1. Who do you think the best actor is?
But when the noun phrase is quite long, some (but not all) speakers are uncomfortable with the long wait for the verb, and use your first structure instead, e.g.
2. Who do you think is the best actor in the history of French cinema?
However, you will never hear:
3. Who do you think is he?
(Which perhaps demonstrates that the structure in #1 is the standard.)