How to get maxima of rho in hough table
Why don't you try to mask your data first. E.g. take the variance for every $\theta$ value, so that you get a $\rho$ variance information for each $\theta$ value. Variance should be high around your peask, since all the other parts are basically black or gray - only in the peak region there is a lot of changes. You could also play around with a auto-correlation of the data along that axis. Then, you could threshold the resulting vector so that you have a better estimate where the peaks are. Then apply the peak detection algorithm only in those areas of $\theta$.