You can use both sentences if you are male. If you are a woman, you can't say 僕（ぼく）. However, there are slight differences between these two sentences. The first one, 何で僕は目立ってないんだ？, has a kind of meaning that you feel a little bit disappointed, you are frustrated or you had expected a lot of attention from others. For example, you wear an excellent costume for a Halloween party thinking you draw everybody's attention, but no one cares about your costume. The second one, 何で僕は目立ってないのかな？, means that you are just asking someone why you are not standing out or you just wonder why you are not standing out. It doesn't imply your frustration. "I wonder if anyone will notice me?" means 誰（だれ）か私（僕）に気付(きづく)くかな？

Hi Sarah - for what it is worth, my teacher just introduced me this week to the end of sentence particle かしら　which is used (only by females) to add, "I wonder" at the end of a statement. Perhaps you could look into this and see how to use it. I won't presume to offer advice on any other part of your query though - will leave that for a native speaker! がんばってください。