MySQL: How do I limit or prevent caching for specific tables?
InnoDB and MyISAM already use different buffer/cache structures, so if you use different engines for the two tables it is very easy to configure different cache sizes.

For InnoDB you set up innodb_buffer_pool_size which caches data and indexes.
For MyISAM you configure key_buffer_size for buffering indexes. MySQL leaves MyISAM data caching to the OS to manage. You could also create custom key buffers for each MyISAM table and decide how big the cache is.