Go to your runlevel directories, normally /etc/init.d/rc2.d, /etc/init.d/rc3.d and /etc/init.d/rc5.d. There you will find symlinks like this:
S[number]ispconfig_server -> /etc/init.d/ispconfig_server
The number is important for the order in which services start at boot time - the higher the number the later they start. If you rename the link to S99ispconfig_server
(S99ispconfig_server -> /etc/init.d/ispconfig_server
) then ISPConfig should start after MySQL.