Backup and restore application preferences
Your preferences will be copied if you allow Migration Assistant to copy your data from a Time Machine backup (one of the options at the beginning of the installation).

Time Machine backs up just about everything except Mac OS X and other system resource files. So, your preferences will be saved.

I've tested this migrating from 10.6 to 10.6, and I've migrated from another Mac directly from 10.6 to 10.7. That process is, in practice, the same.
So, your preferences will be copied from your Time Machine backup to your new system.