samtools view -b input.sorted.bam `samtools view -H input.sorted.bam |grep "^@SQ" |cut -f 2,3  |sed "s/.N://g" |awk '{if($2>1000){print $1}}' |tr "\n" " "` > input.longcontig.sorted.bam

Check the output of samtools idxstats. It gives you in a tab-delimited format the name of the chromosome, chromosome length and the number of reads mapping to it. It requires an indexed BAM file. The output is easily parsable and it is fast since it relies on the index.