There is no standard way AFAIK. However, some terminal emulators allow control using DCOP and similar tools. For example, the KDE terminal emulator, konsole, may be resized by making a function call via dcop like this (example is using command-line dcop tool, but there's a C API to make dcop calls).
Code:
dcop konsole-4695 konsole-mainwindow#1 setSize 800x600
The -4695 is the PID of the konsole instance in question.