The base commander one kind of stands out but not necessarily in a good way. First, because it is the only military LOR per say, who is the Base Commander to you? Does he have anything to do with your career field? Are you prior enlisted? If you're prior why not get more from military members. Is he a family friend (because that will make it less valuable imo).. How well does he know you?
Def keep it though, because it will pull some weight, but all I am saying is don't use an LOR from a C/O from the USAF to the Navy and expect it to make a big difference if he's family/family friend or what not. So I'd get at least one more solid one.
I got one from my congressman, and frankly I think the one from my Chief in the USAF holds more weight..
If you're prior enlisted and he is your base commander then golden.. Just get another from your supervisor or squadron C/O and I'd call it good. On the other hand, I had gotten an interview with a Naval base commander and he is a Naval Aviator as well... See where I'm going with this?