It all depends what your preferences are. We didn't care much for Chaweng. It's very commercial and busy. Bo Phut is lovely, our favourite resort on Samui.
Having said that, and had a good look around Samui, I would choose Krabi every time. We were based in Ao Nang, which in itself is quite busy, but nothing compared to Chaweng. Ao Nang is a good starting point as there are loads of beaches and islands within a few minutes boat ride, many of which have cheap accomodation to rent for a night or two, some of which are very quiet.
I guess Samui has been doing the whole tourist thing a lot longer than Krabi, so you would expect it to be more built up. We did have a great time there and would go back, but Krabi does it for me.