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I have two models, A and B. I have performed 10-fold cross-validation on both of them, so now I have 10 $R^2$ scores for each.

How can I determine whether one is significantly better than the other? I fear that calling $A$ the winner iff $$\text{mean}(A)-\text{SEM}(A) > \text{mean}(B)+\text{SEM}(B)$$ is perhaps not the correct way to do it.

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Well, assuming all of your modelling assumptions are fulfilled, the modelling techniques do not differ and also assuming $R^2$ is the only model characteristic that differs between the models, I would consider a Student’s t-test (assumptions permitting) or Wilcoxon-Mann-Whitney test on the $R^2$s. In any case I would try to get a larger sample (costs permitting).

You can read more about different model selection measures, particularly AIC, here.

If different modelling techniques were used you may find this interesting.

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