Given a set of intervals and a set of peaks with some score value, you could use BEDOPS bedmap --max-element or bedmap --max to get the maximum scoring peak over the interval, or just the maximum score, respectively:

$ bedmap --echo --max-element --delim '\t' intervals.bed peaks.bed > answer.bed

If you're looking for measured size or other peak features, there are other operators like --echo-map-size, --count, etc. that offer mapping of those results. Feel free to clarify what you're after, or take a look at the documentation or bedmap --help.

Im working on ATAC-seq data at the moment.

I've used ChipPeakAnno to annotate the peaks in the narrowPeaks file (MACS2 output) for genomic features (TSS etc). You could then do a simple count of the number of peaks annotated for each feature.

Have you considered using DESEQ2 for getting differential peaks first? That is a far more sophisticated package for comparing samples.