This is a good question, but it shows once again the difficulty of assessing the options without knowing the context. I think we can assume we’re talking about speech and not writing. If so, what is said will be reinforced by paralanguage and tone of voice and may not occur in exactly the same way that we might write it.
‘If you are going outside, please let me know’ is a well-formed sentence, but the extent to which it is or isn’t polite will depend on the circumstances in which it is said and the way it is uttered. Imagine a workplace or a classroom. If someone repeatedly went outside without permission (person A), a teacher or supervisor (person B) could say ‘If you are going outside, please let me know’ as a rebuke, particularly if staring hard at the offender. If, on the other hand, B was merely making a request of A, then the words might be formulated a little differently, as, for example, ‘Oh, look, by the way, I’d appreciate it if you’d let me know if you’re going outside, because I need to know where everyone is’ and it would be said in a friendlier tone and with less aggressive body language.
Of course, the situation might be one in which B wants to ask a favour of A, such as asking B to bring back something from outside. In that case ‘I was wondering, if you were going outside’ is perfectly possible, but so, too, is something like ‘You’re not going outside by any chance, are you?’ It is, however, hard to imagine any circumstances in which ‘If you were going outside, please let me know’ might be used. That sequence of tenses is not normally used in a conditional sentence.