[I thought I had written an answer to the first question but I can't locate one.]
With 5 or fewer observations, you might as well just plot the actual points.
It doesn't matter when comparing across samples that the samples aren't the same size, but if you have much larger samples in some groups you should see more points outside the ends of the whiskers on those.
what is the best way to compare between methods with different sample size
You might compare quantile plots, perhaps, or (as Nick Cox has suggested on at least one of his answers, but which I also can't locate right now -- edit: see here) you might combine such a plot with a boxplot by plotting the quantile plot under the boxplot.
Nick shows an example of a quantile plot here