I think you've partially answered your own question, but I'll add my 2 cents worth The "best" application is pretty subjective...it depends on your level of skill & preference. For wireless work, I use Kismet for general recon, and use the aircrack suite for detail stuff. I use nmap a lot; it's very versatile & powerful, no matter the network. In terms of password cracking (against hashed passwords), I use rainbow tables.
If you're really wanting to get some wireless pen-test knowledge, I'd take the course offered at Offensive Security.