use warnings;
use strict;

my $N = 3;
my $new = "NEW";

while (<DATA>) {
    my @words = split /\s+/;
    $words[$N-1] = $new if scalar @words >= $N;
    print join " ", @words, "\n";
}

__DATA__
hi there everyone I am looking to substitute
lots of words for new ones, but only the third
word per line on each line!
one
one two
one two three
one two three four