When you say I am wondering, you are usually thinking about the possibility of something. When you say I think, you are usually just stating something you believe. I thought is simply the past test of the verb "to think".

I wondering does not exist. You would say "I am wondering", and that means you are thinking about something. I thought is the first person past simple of I think.

I think is present tense (right now you are thinking something). I thought is past tense or something you thought would occur. I wonder is like to imagine something that has not yet happened.