Note: This thread is meant to be beginner friendly. If you are an advanced learner, please be kind by putting furigana on the LV6+ kanji by using the following html!
が emphasizes 弟.
It sounds like you were already talking about who is funny, of all people or among some people, and you are stating you think your brother is THE funny person.
を marks object
This を marks object. In this case, who you think as a funny person. This sounds neutral, stating that you think your brother is a funny person now.
は marks subject
This は marks subject, so grammatically, there is a subtle difference between 2 and 3 as seen below, but it’s also a correct particle choice.
(私は)今は弟を[面白い人だ]と思っています。
(私は)今は[弟は面白い人だ]と思っています。
I chose 2 over 3 because 3 could sound like you think that your brother is a funny person as a general statement, whereas 2 is more clear that you think your brother as a funny person.