Lex Luthor the self styled "Greatest criminal mind of all time!" would easily take the top spot. He is often shown to be more intelligent than any other human, and even more so than some super intelligent extraterrestrials.
As for the second there are several characters who could lay claim:
Brain, perenial thorn in the Doom Patrol's side has pulled off "Perfect Crimes" on several occasions.
Barbara Gordon in her pre-New 52 Oracle persona, as stated by Bill the Lizard, definetly quallifies.
Noah Kuttler aka the Calculator is the villanous counterpart to Oracle and could also qualify.
Lastly a tie between two masters of deductive reasoning and latteral thinking;
the Riddler is often stated to be Batman's most intelligent adversary.
Ralph Dibny has been shown to be a detective with an intellect to rival that of Batman.