Code it in Perl then ...

#!/usr/bin/perl -w
use strict;
my @mega = (
                  ["AGCT", "0", "370",  "1"],
                  ["AGGT", "3", "52",   "1"],
                  ["TGAA", "2", "233",  "0"],
                  ["AGAG", "0", "32",   "0"]
                );

open ( fh, ">junk.txt" );
for my $row (@mega) {
        print fh (join ":", @{$row}) . "\n";
}
close fh;
my $shellout = <<`SHELL`;
sort -n -t: -k2,4 junk.txt
SHELL
print "$shellout\n";
[download]

... if you expend some effort you can find away of avoiding writing the array to a file as sort does accept input form STDIN also, read the man page.