The answer is "He wondered what the time was". ->To understand clearly,we can rewrite the context like this: "What is the time?",he asked/wondered.(This is the direct speech) =>"He wondered what the time was."(This is the indirect/reported speech)

Yes,because it's not a question so you should say he wondered what the time was

..

Please write "please" correctly next time!

He wondered ... the time was. As for explaining, the rule is too elementary. Check out indirect questions. Do you know what the time is? Did you know what the time was? He told me what the time was. You haven't told me what the time is.