People often use the first one out of politeness when asking a question: Ex. I was wondering if you'd like to join me for lunch? You can also use it for "wondering" in the past. Ex. I saw the store and was wondering if it was closed. I'm wondering if I should go to the movie. (I haven't decided) Also possible: I wonder if I should go to the movie.

The difference is simply that "I am" is present tense and "I was" is past tense. However, in ordinary conversation you would often use "was" even though "am" would be logically correct: for example "I was wondering if it will rain today and if I should go for a walk."