Marvel - I'll stick with Sue.
DC - Oracle and Tala are prety clever and can think well on their feet.
I think you should also state what you mean by "smartest." Do you mean academically smart or how well they can analyze situations? For instance, Reed Richards' knowledge of science is a lot more than Batmans but Bruce can outsmart anyone at any given time.
marvel--ultimate sue, she's just 19 and she's got doctorates in 4 sciences, plus in 616 reed regularly bounce ideas off her, or at the very least, she understands everything he's saying when he's eambling on about some high end thoery
DC--im tempted to say Steeel's niece cuz she's a super wiz and she did design and build her own armor after all, plus b4 it turned out that star labs couldnt be trusted she was working there and she still in her teens