You can put whatever score you want to, as long as it's honest, because reporting AP scores is not required on applications (unlike ACT, SAT, and sometimes SAT II). I can't cite any source except for my college application adventures with Common App, but yes, you can choose to list some scores and not other scores. AP scores don't even come into play until you're going to a school and you want to exempt classes.
Bottom line, what you make on the tests is not important, the fact that you took the course and did will is the important thing. Anything 3 and above, don't be ashamed to report it.