Conditions for choosing quantifying and qualifying ion in LC-MS/MS
The limit of detection (LOD) in these kinds of assays depends on both the noise and the signal.  Usually it is defined as lowest concentration analyzed such that the signal (peak height) is three standard deviations higher than the noise.  Exactly how to define "the noise" is a critical consideration -- many different sources provide different definitions and ideas.  The best measurement of "noise" is probably in a method blank at the exact RT window you are using for quantification.  Ideally the method blank would have a sample matrix identical to your real samples, but guaranteed to be missing the target compound.

It's a little tough to know from the information provided in your question how exactly you are calculating your LODs.  If for the moment we assume you are happy with how your LODs are computed, then I would pick the method with the lowest LOD.

It's also worth mentioning that a standard practice in targeted LC-MS/MS is to monitor two separate transitions per compound.  One of those is called the "quantifier" and it is this signal that is used to compute peak areas for quantification.  The other is called the "qualifier".  The ratio of the qualifier peak area to the quantifier peak area should be monitored for all analyses, and it should be approximately the same for all samples (that contain measuremable compound).  If this ratio deviates wildly, it's a sign that the quantifier ion may not be reliable for a particular sample.