Charizard. Period. Charizard is much higher than Sceptile. Charizard has most likely been alive longer, has been in more battles, has trained more (with ash, and at the charicific valley, which would boost its power MUCH more.), and has a MUCH bigger determination to be the best. I doubt it would ever give up in a battle, unless it was actually physically impossible for it to move. It never wants to lose.
Edit: Wow, after readint this thread, I can believe anybody can ever compare Sceptile to Charizard. Same with Pikachu. There is no way Pikachu could come close to surviving a battle against Charizard, and most likely against most of Ash's other pokemon. Just because he's had it the longest doesn't really mean anything in this certain case. It's endurance sucks in battle. It is knocked out after 3-4 attacks.
Think of the battle with Gary's Eevee. If Pikachu lost to a brand new Eevee, that can't mean it's that much powerful.
Believe me though, I'm not a "Charizard only Fan", I just can see that Charizard is obviously going to be Ash's best pokemon for as long as it lives. If it keeps it up, Sceptile can't pass it up.
As for Ash's second best, I'm not sure. snorlax, Heracross, or Sceptile come to mind. I'm not sure why Heracross does though. It just has a spunk to it.