I have had both honestly. A crippling stomachache makes you feel like you're being torn apart from the inside out. When you add terrible nausea to the mix, there were so many times I could have just passed out and wished to stay out. You feel like you're about to just explode and implode at the same time.
However I've also had a really bad toothache before. And that just feels like hell in your mouth. You can't rub it, you can't put a warm compress on it. All you can do is lay down and cry in pure and utter agony. If you have an open tooth nerve and you can't find a dentist, all you can do is pray that something stops the pain.
In my personal opinion I feel like a toothache is worse, just by a little bit. While a crippling stomachache can make you want to just... well...not exist anymore, you can at the very least gain some sort of relative comfort in a warm compress, some soothing tea, or even massaging your stomach. A toothache... there is very little you can do that'll ease the pain. You can place Orajel on it or takes TONS of Novocaine, but these almost never work for me. And enough of it just makes me feel like there's a hole in my face.