Follow the Ubuntu RcLocalHowto to create
/etc/init.d/local, and then put your command in that file. The mount will then happen automatically on boot.
To test, invoke
/etc/init.d/local manually on the command line (as root). You should see that causes the mount to occur.
EDIT: doing the mount from /etc/fstab should work fine too, according to the s3fs faq:
s3fs#example.com /mnt/s3/blah fuse _netdev,use_cache=/tmp,use_rrs=1,allow_other 0 0
Reason to prefer the /etc/init.d/local approach: it's simpler to set up, just put your existing mount script in that file.
Reason to prefer the fstab approach: it's a more standard way to do mounts, and someone who doesn't know about your setup can just look in /etc/fstab to determine what mounts your machine is making.