Thanks for your input so far. Here is a sample chromatogram:
I have the "small peak" compound available in  pure form, so I can easily calculate the LOD/LOQ with no obstructing peaks. It just seems like the value is too low for the sample matrix shown in the chromatogram above. 
As for the slope of the calibration line/standard error method -- wouldn't that method also underestimate the LOD/LOQ in this case?
Do you have the "big" peak also in pure form?
Otherwise you can do an accuracy test, and see if there is a significant bias. If so, the method isn't sufficient to quantitate the minor peak, and you can't determinate an LOD/LOQ (or an amount....)
If it is accurate, the slope/se method wil be good enough to estimate the LOD/LOQ.
If you are afraid to underestimate, you can integrate valley to valley, this will overestimate your LOD/LOQ.
Bart