It's true that the tense is different (past/present), but in fact they are used almost interchangeably. The main difference is, "I was wondering..." means that I have been wondering about something for a little while (but it could be a very short, like a minute or two). With "I am wondering", it means that I am wondering now, and it might, or it might not be a new thought.
You might also just say, "I wonder..."
"I wonder what you think of this book." [I'm curious about your opinion.]
"I'm wondering what you think of this book." [Your opinion is something I'm thinking about. And I'm curious.]
"I was wondering what you think of this book." [I have been thinking about your opinion for some amount of time. And I'm curious.]