"你在忙什么"怎么问?

what are you busy with ?
what are you busy doing ?

两个都不好！也可用现在完成时的句型来问。
What have you been busy?"你都在忙什么"

这样最好的说法；"What are you up to?“你在忙什么？”

若要用你的话就这样：
“What are you busy with?”要加 with

what are you busy with (these days)?
what are you busy doing?也可
最好用可以表示延续性的表述

1 What are you up to?
2 What are you doing?Are you busy?

What are you busy doing?

what are you busy in ?