The UFC and Strikeforce are two totally different organizations although they are both using the same sport... mma (mixed martial arts). Not comparable to AFC/NFC, which are two conferences in the same org.
Strikeforce is run by Scott Coker (their CEO) and owned by Silicon Valley Sports. The UFC is run by Dana White (their president) and owned by Zuffa (which is run by the Fertitta bros.)
Concerning who's the best fighter, that is really subjective especially since it's so unlikely to ever see Fedor compete against the best in the UFC. But to find the best fighters in different weight classes, this thread by IronMan contains the closest thing to consensus rankings I've ever read: